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The classic story regarding the evolution of antibiotic resistance that is taught to students at more-or-less all levels is that the presence of antibiotics - in growth medium, in an infected organism, etc. - kills off the susceptible bacteria, leaving resistant members to survive. More complex versions of this story note that early resistant mutant phenotypes tend to somewhat sensitive to antibiotics, and as more and more generations appear, the resistant phenotypes become more and more resistant, finally culminating in resistance to antibiotics at dosages that are utilized clinically.

Though quaint, plausible, and powerful with respect to explanatory scope, the story is simply not true. It has been known for a good deal of time that most antibiotic resistance genes are acquired and passed to other bacteria via integrons, which are mobile genetic elements that can capture and transfer genes, and subsequently integrate them into other genomes in a site-specific manner. For the most part, antibiotic resistance in bacteria is a consequence of both inter- and intraspecies transfer of non-essential, self-replicating, extrachromosomal collections of genes and other elements of DNA information known as plasmids. An excellent article detailing this information was published in the journal Cell back in March of 2007.The abstract from this article nicely summarizes and supports what is written here (special emphasis added by TRR):

Molecular Mechanisms of Antibacterial Multidrug Resistance Cell 128(6):1037-1050 Michael N. Alekshun and Stuart B. Levy Treatment of infections is compromised worldwide by the emergence of bacteria that are resistant to multiple antibiotics. Although classically attributed to chromosomal mutations, resistance is most commonly associated with extrachromosomal elements acquired from other bacteria in the environment. These include different types of mobile DNA segments, such as plasmids, transposons, and integrons. However, intrinsic mechanisms not commonly specified by mobile elements—such as efflux pumps that expel multiple kinds of antibiotics—are now recognized as major contributors to multidrug resistance in bacteria. Once established, multidrug-resistant organisms persist and spread worldwide, causing clinical failures in the treatment of infections and public health crises.... The means that microbes use to evade antibiotics certainly predate and outnumber the therapeutic interventions themselves. In a recent collection of soil-dwelling Streptomyces (the producers of many clinical therapeutic agents), every organism was multidrug resistant. Most were resistant to at least seven different antibiotics, and the phenotype of some included resistance to 15–21 different drugs...

So... not only is antibiotic resistance, in general, not attributable to mechanisms of Darwinian evolution (random selection of 'more fit' individuals via the influence of some multitude of 'selective forces'), but the mechanisms that microorganisms commonly use existed prior to the use of antibiotics.

This is actually summarized quite nicely in a story (Medical Tribune, 29 December 1988, pp.1, 23, no electronic resource known to be available) about some unfortunate sailors who froze to death on an Arctic expedition back in 1845. The sailors were buried in the permafrost until 1986 when their bodies were exhumed. Given that the sailors had been frozen solid in the permafrost, the bodies were extremely well preserved; in fact, researchers were able to isolate and revive six strains of 19th century bacteria found within the contents of the sailors' intestines. These 19th century bacteria - bacteria that were alive prior to the discovery of penicillin were found to be resistant to several modern-day antibiotics, including penicillin.

Another piece of research has appeared that further corrupts the classic story of the development antibiotic resistance via Darwinian evolution. The abstract is reproduced below:

Integrons are found in the genome of hundreds of environmental bacteria but are mainly known for their role in the capture and spread of antibiotic resistance determinants among Gram-negative pathogens. We report a direct link between this system and the ubiquitous SOS response. We found that LexA controlled expression of most integron integrases and consequently regulated cassette recombination. This regulatory coupling enhanced the potential for cassette swapping and capture in cells under stress, while minimizing cassette rearrangements or loss in constant environments. This finding exposes integrons as integrated adaptive systems and has implications for antibiotic treatment policies.

You got all that, right?

Perhaps not. I'll do the best I can do translate it: This particular article details the molecular mechanism behind the transfer of resistance genes between bacteria. As the article details, it's the use of antibiotics themselves that actually triggers the synthesis of a specific bacterial enzyme that identifies and preferentially captures the resistance genes, and subsequently facilitates their expression. Additionally, this enzyme promotes the rearrangement of these resistance genes. The rearrangement of these genes alters the order of when the genes are expressed. New rearrangements that are triggered by taking an antibiotics, and those bacteria that have 'correctly' rearranged their genes, creating a new resistance cassette, will be able to survive and pass on resistance not only vertically, to subsequent generations, but also horizontally; bacteria can pass resistance genes to their neighbors in a deliberate manner.

This is huge. The classic Darwinian story render the organism entirely a slave to the environment, unable to respond or adapt at the individual level. Only a lucky few - a few that are resistant simply by chance - survive the selective pressure of antibiotic use, and are able to pass on their genes.

Or as you've been more simply taught: Survival of the fittest.

This new research clearly indicates that this is not necessarily the case; indeed, it appears that - contrary to what I've been taught more-or-less through my entire history in science - individual organisms, not just populations are able to react to and adapt to the environment.

Or at least individual microorganisms are able to do this.

It cannot be stressed enough how significant of a break this is from the classic story of antibiotic resistance via Darwinian evolution. The idea that the individual and not just the population of organisms can adapt to a changing environment at the DNA level is literally scientific heresy.

This is of course more evidence, another huge piece of evidence suggesting that The Theory of Evolution with respect Darwin's ideas is at least not as well understood as was once believed, and at most completely, utterly, and totally false.

Even a broken clock is correct twice a day. Amid outlandish and perhaps... pitiful gaffes such as confusing the name of the Justice who swore him in only a day earlier, miscalculating the number of letters in a three or four letter word, and the possibly Vice Presidential precedent setting gaffe containing two misstatements in a single sentence, claiming first that FDR was President when the stock market crashed, and that he didn't go on the TV and simply "didn't just talk about the, you know, the princes of greed", apparently unaware that the TV wasn't available to the general public at that time. Among the hysterical proclamations regarding relatively a, thus far, relatively innocuous out of season flu, and even after the self-deprecating statements regarding his inferior qualifications for the Vice Presidency relative to other possible candidates, even Joe Biden, however infrequently, offers us a bit of wisdom from time to time. What could I possibly be referring to (Source)?

Sen. Joe Biden, D-Del., on Sunday guaranteed that if elected, Sen. Barack Obama., D-Ill., will be tested by an international crisis within his first six months in power and he will need supporters to stand by him as he makes tough, and possibly unpopular, decisions.

Biden was right; Obama has been tested, he's been tested multiple times in fact. Unfortunately for the United States, his response to each crisis has been ineffectual, and ultimately have presented a posture of weakness to rest of the world. Let's examine a few specific instances.

Shortly after taking office Obama indicated that he was willing to re-establish diplomatic relations with Tehran if Iran would "unclench its fist". This is in stark contrast to GWB's policy with respect to Iran; he refused to hold talks with the the "axis of evil" nation until it suspended enrichment of uranium. Iranian President Mahmoud Ahmadinejad responded by launching a tirade against the United States, demanding apologies for its crimes against Iran, and stated that he expected "deep and fundamental" change from Obama. Ahmadinejad further stated that "[Obama's] request means Western ideology has become passive, that capitalist thought and the system of domination have failed..." he further added that "Negotiation is secondary, the main issue is that there is no way but for (the United States) to change...". Tehran has subsequently violated the Nuclear Non-proliferation Treaty that it signed and announced that they have successfully mastered all the steps essential to enrich uranium, and is now in possession of enough to construct a nuclear weapon. Despite these statements and clear violations of a treaty that Iran signed, Obama still believes he can trust Iran's word, or at least should trust it for the near short-term:

President Obama said Monday that he expected to know by the end of the year whether Iran was making "a good-faith effort to resolve differences" in talks aimed at ending its nuclear program, signaling to Israel as well as Iran that his willingness to engage in diplomacy over the issue has its limits. "We're not going to have talks forever," Mr. Obama told Prime Minister Benjamin Netanyahu of Israel after a two-hour session in the Oval Office.

Iran has made it abundantly clear in the past that they have no intention of ceasing uranium enrichment or ending their pursuit of nuclear weapons; this was affirmed again this week when Iran rejected an offer to stop all nuclear work in return for no new sanctions. Iran also ruled out any further talks with major powers on the issue.

In other words, Iran doesn't want to talk, Iran will continue to develop nuclear weapons, while Obama waits until the years end to see if Iran is in compliance by ending its nuclear program - which it has already clearly stated it will not do. Iran's actions clearly indicate - and they've more or less stated - that their nuclear program won't end, but Obama wants to see if they'll make a good faith effort to end it.

Huh? Faith in what?

What scintilla of evidence exists that Iran has any intention of ceasing these activities, or that Iran has even a shred of respect for what Western Leaders think about this issue.

That was of course a rhetorical question; there is no evidence. Indeed, all available evidence suggests that the exact opposite is true.

The situation with North Korea is far worse, and is, in my opinion, much more scary. On April 5 of this year, the North Koreans fired a rocket over Japan that, fortunately, landed harmlessly in the Pacific Ocean. Firing of this missile was carried out in direct defiance of UN Security Council Resolution 1718, which holds that North Korea end all ballistic missile activities. North Korea maintains that this was part of their peaceful space program and that this was merely a communications satellite launch. Many nations, including the United States, South Korea, Japan, and a number of other countries believe that the launch was a long-range missile test.

In fact, since Obama took office this year, North Korea has fired nearly half a dozen missiles - including one that may have the capability of hitting Alaska, Hawaii or the West Coast of the US. Negotiations with the North Koreans have never been productive, and have always been undermined and/or ignored by the North Koreans. GWB learned this the hard way; when GWB re-engaged in diplomatic relations with Pyongyang instead of increasing the pressure on the regime, he not only re-legitimized the North Korean regime, but provided more time to 'bargain,' which apparently when translated to the North Korean dialect means "construct weapons of mass destruction."

North Korea has further defied the world, and indicated that negotiations with the regime are not an option; Negotiations now, as they have in the past, will simply result in the advancement of North Korea's nuclear program. This is supported by the fact that two days ago, on May 25, 2009 North Korea announced they had successfully carried out an underground nuclear test. This announcement was confirmed by geological sensors in South Korea that were able to detect the blast as an artificial tremor. The Russian Defense Department, determined that the blast yield of the second bomb was between 10 and 20 kilotons, which is comparable to the bombs dropped on Hiroshima and Nagasaki at the end of WWII, but significantly more powerful than North Korea's previous test in 2006.

North Korea obviously has no intention of ending their nuclear weapons program, and appears to be scaling it up. Obama, meekly, responded with the following: "North Korea is directly and recklessly challenging the international community... "North Korea's behaviour increases tensions and undermines stability in north-east Asia." Obama is a masterful wordsmith; it's one of the primary things that got him elected. One of the qualities that makes him a great speaker is his preternatural calm.

He is always calm.

It's somewhat counterintuitive, but this ability to always be calm, to be calm under all circumstances is not necessarily a good thing. It's certainly a good thing to be able to maintain your cool, but it's also a good thing to be able to express yourself in a strong and forceful manner. Sometimes this is the only posture that an adversary will respect.

Let's face it Ahmadinejad does not respect Obama as a leader, and perceives this calm, his desire to negotiate as weak.

Recall that JFK had a similar experience with Khrushchev, which in all likelihood started the Cuban Missile Crisis. Like Obama, JFK was eager to negotiate with his enemies, in this case, the U.S.S.R.. Recall Kennedys quote regarding this issue: "Let us not negotiate in fear; but let us not fear to negotiate." Kennedy and Khrushchev met in June of 1961. Following the meeting, JFK stated that this had been the "roughest thing in my life. He just beat the hell out of me. I've got a terrible problem if he thinks I'm inexperienced and have no guts." Khrushchev recorded in his notes that Kennedy was "too intelligent and too weak."

An intelligent and weak leader... hmmmm... sound like anyone we know?

Khrushchev responded by closing the previously open borders between East and West Berlin. The Kennedy administration responded to this by engaging in "polite protests" against the Khrushchev's actions; Khrushchev responded by building the Berlin wall. Kennedy's weak and ineffective responses emboldened Khrushchev such that he assumed he could get away with placing nuclear missiles in Cuba.

Recall how both the Cuban Missile Crisis and the division of Berlin were resolved; they were resolved by negotiating from a position of strength. Kennedy resolved the Cuban Missile Crisis by exerting strength, not a willingness to further negotiate. Kennedy initiated a naval blockade on Cuba, backed with the force of U.S. war ships that threatened to fire on any ship that tried to subvert the blockade. It was only after this show of strength that Khrushchev backed down. Recall that Ronald Reagan, with his hardline stance against the Soviet Union throughout the Cold War was able to not only reunite, but Berlin, but was able to end the Cold War and Soviet Communism.

In short, Obama's policy of negotiating with megalomaniacal dictators is ill-conceived, and stands in opposition to well-established historical facts and precedents. In addition to the above examples, we have the experience of Chamberlain and Hitler. Chamberlain was British prime minister from 1937 to 1940. Having lived through the 'Great War,' Chamberlain was determined to avoid involving Britain in another war. His policy of Nazi appeasement resulted in the Munich Agreement, which ceded the Czech region of the Sudetenland to Germany. Believing that he appeased Hitler, Chamberlain left Munich feeling that he had assured 'peace for our time'. Hitler of course responded by annexing the rest of the Czech lands, Bohemia and Moravia, and rendering Slovakia a German puppet state. Nearly 6 months later, Hitler invaded Poland. Chamberlain was forced to respond declaring war on Germany.

Each of these examples should serve as a lesson to President Obama; we can prevail only from a position of strength. We do not negotiate with dictators and tyrants; history proves that this is an ineffective way to deal with evil. We prevail only when we firmly communicate our position, and firmly communicate that we will utilize whatever means are necessary to obtain our goals, and maintain our national security. Khrushchev taught JFK, and indeed the world a invaluable lesson; despite what Kennedy naively believed, sometimes we must in fact fear to negotiate.

I just found this article on Bloomberg.com regarding the H1N1 Swine Flu; the article is entitled: "Swine Flu Is Spreading Wider Than Official Data Show (Update2)", and this article is nothing more than scare tactics and sensationalist journalism at its worst. It might take a trained eye to catch some of this stuff and interpret it, but that's what I'm here for. In any case the first little bit of the article reads:

Swine flu is spreading more widely than official figures indicate, with outbreaks in Europe and Asia showing it's gained a foothold in at least three regions.

This first statement is meant to frighten you, meant to lead you in and make you believe that the swine flu is a serious concern - or at least more or a concern than the typical seasonal flu. The italicized portion is the real scare tactic... in reality it's actually quite an innocuous statement, and is explained in the very next paragraph/statement:

One in 20 cases is being officially reported in the U.S., meaning more than 100,000 people have probably been infected nationwide with the new H1N1 flu strain, according to the Centers for Disease Control and Prevention.

Sounds scary, doesn't it? In actuality, it's not only not a bad thing - it is in fact a good thing, and here is why. In my previous swine flu update, I provided some statistics regarding Case Fatality Ratios (CFR's) for not only past 'serious' flu outbreaks, but also for the seasonal flu, and this current swine flu outbreak, rather than reproducing these statistics here it is easier to simply quote this other post:

...the CFR is the best estimate or description of a disease's virulence. Estimates for the CFR of the seasonal flu are approximately 0.1%. The 1918 Spanish Flu Pandemic has been estimated to have a CFR ranging from 2% to 20%, depending on which sources you check, but is most commonly given as 2.5%. This particular virus, depending on which statistics you look at. Considering only the number of deaths per infected individual, the USA, Mexico, and worldwide have CFR's of 0.110%, 1.97%, and 0.78% respectively. These CFR's are likely overestimated as well; it's reasonable to assume that the actual number of cases is higher – probably significantly higher – than the reported number of cases.

As the quote above indictates, the CFR's that I have calculated are actually likely to be overestimated by at least an order of magnitude, or as suggested above as much as 20 times. If I recalculate CFR's based on an underestimate of 20 fold, the numbers as of today for the USA, Mexico, and the entire globe are 0.00739%, 0.09635%, and 0.036525%, respectively. In the worst case scenario, Mexico, based on the most recent swine flu update from the WHO, the approximate CFR is 0.09635%, under the value typically estimated for the seasonal flu. If you read the article a bit further, the prognosis is even more hopeful:

In the U.K., the virus may be 300 times more widespread than health authorities have said, the Independent on Sunday reported yesterday.

Or based on the most recent numbers of 137 cases and 0 reported deaths, the actual and estimated CFR's are zero, given the underestimation of the case number, the number is less than in the US or Mexico when each of those countries had a comparable number of cases 0.709% and 5.769% for the US and Mexico, respectively. Even more good news:

Japan, which has reported the most cases in Asia, began reopening schools at the weekend after health officials said serious medical complications had not emerged in those infected.

The statement that follows attempts to frighten the reader once again:

The virus is now spreading in the community in Australia, Jim Bishop, the nation's chief medical officer, said yesterday. "I think we will see the number rise," Bishop told Australian Broadcasting Corp. radio today after confirming the nation's 17th case and saying test results are pending on 41 others.

The flu virus spreads, and as it spreads, the number of cases rise; this is what's expected of the flu virus, or for the most part, any easily transmitted virus. As the virus makes its way around the planet, more people are infected. Nothing scary about that - or at least nothing more scary than the seasonal flu. The statement that truly drives home the point that - thus far - there is nothing to fear from the dreaded H1N1 swine flu:

Most of those infected experience an illness similar to that of seasonal flu. The main difference is that the new H1N1 strain is persisting outside the Northern Hemisphere winter.

For the most part the rest of the article simply cites statistics about the virus - all of which suggest that this particular virus is of no more concern than the typical seasonal flu.

If this most recent foiled jihadist terror plot doesn't give you pause; if this recent near-incident doesn't clarify for you the nature of the enemy we are fighting, and if this evil, backwards, morally distorted plot to blow up synagogues and shoot down military aircraft, right here, - AGAIN on US soil - doesn't further drive home the fact that we are at war, we are at war with not just Al Qeada, and not with Islam, but with a radical ideology that would see your wives, daughters, and sisters raped and enslaved, and your husbands, sons, and brothers tortured, slaughtered, and beheaded. We are at war with a totalitarian ideology that doesn't believe in freedom of speech, freedom of religion, or most forms of freedom of expression; a totalitarian ideology wherein it is more honorable for a father to shoot his daughters then let them have boyfriends, or where "prominent" members of the community behead their wives because the wife files for divorce.

For those of you who've been living in isolation for a week or more - or for those of you who get your news from the NY Times or CNN, briefly, this is what occurred (Source):

Three Americans accused of plotting to blow up New York synagogues and destroy a US military plane are fanatics "eager to bring death to Jews", a court heard... The three suspects - James Cromitie, David Williams and Onta Williams - were held in a raid as they planned to destroy two synagogues and fire a Stinger missile at a plane... New York police chief Raymond Kelly said the four, all US citizens who face life in prison if convicted, "stated they wanted to commit jihad," or Muslim holy war... The alleged plot was dismantled after a year-long FBI undercover operation in which the suspects were sold a fake missile... Snyder described the gang's intentions as "a plot to bring mass murder" and to "destroy military aircraft and kill military personnel".

There are many noteworthy items in the above quote - things that could written about at length. But to a certain extent, foiled terror-plots, and homegrown jihad are old news. Way back in 2005, the Bush administration claimed to have foiled at least 10 terror plots, and since 2005, I'm sure they'd claim even more.

So, as Americans, we've come to expect foiled terror plots. Thus far 9/11 has been the exception not the rule.

How long it remains the exception is a function of our vigilance as a population, but also as a function of a government - an internal security structure that takes these things seriously. With respect to the population: I think the populace would be concerned if they had an accurate picture of what is actually happening in this country. Let's start with the mainstream media. The above comment about the NY Times and CNN was half tongue-in-cheek. I say half tongue-in-cheek because those outlets certainly reported on this case, however - as is typical of the mainstream media - most news outlets, including the NY Times and CNN, refuse to acknowledge that this was a jihadist plot; the men who were going to carry out this slaughter of innocents were Muslims - homegrown petty thieves, converted to radical Islam while in prison.

Robert Spencer gives a great interview concerning jihadist recruitment in US prisons, and according to Spencer the problem is significant; it is in fact a large scale effort that is funded by not only the Saudis, but also the Islamic Society of North America, the former speaks for itself, while the latter have been associated with Hamas. According to Spencer not only are the prisons unaware of this, but wouldn't know how to look for it or detect it if and when it does occur.

The SkyNet article details that these men lived Newburgh, NY, which is about 60 miles outside of NYC. Newburgh, NY is also about 150 miles from Hancock, NY. For those of you not up on your Islamofascism in the USA, just outside of Hancock, NY there is a terrorist training camp, affectionately known as Islamberg. This camp is run by a group called Jamaat al-Fuqra, whom you may or may not have heard of. Perhaps the most noteworthy and notorious mention of Jamaat al-Fuqra is via beheaded journalist Daniel Pearl; when Pearl was kidnapped and subsequently beheaded, he was on his way to meet Pakistani Sheikh Muburak Gilani, the leader of Jamaat al-Fuqra.

Jamaat al-Fuqra, has a long and sordid history however. US officials have linked the organization to at least 17 homicides and 13 firebombings within the US; its targets were often rival Muslim leaders. In July of 1983, an al-Fuqra member named Stephen Paul Paster set off a bomb at the Hotel Rajneesh in Portland. In 2003, a member of Jamaat ul-Fuqra, Lyman Faris, pled guilty to plotting to blow up the Brooklyn Bridge. Perhaps even more frightening than this is that the US Department of Justice has reported that Jamaat ul-Fuqra maintains "more than 35 suspected communes and more than 3,000 members spread across the United States, all in support of one goal: the purification of Islam through violence."

The activities of Jamaat al-Fuqra, and the specifics of what occurs in these camps has been frighteneningly detailed in a new documentary from the Christian Action Network (CAN) called Homegrown Jihad: The Terrorist Camps Around the U.S.. According to this documentary, the CAN spent two years visiting many of these compounds, oftentimes with substantial personal risk. The documentary states that these camps run by Jamaat al-Fuqra are specifically dedicated to the training of Muslims in jihadist/terrorist activities. The camps are largely tucked away in remote rural areas where they can be left alone, and given what is happening on the inside, this is no surprise. A promotional/marketing video obtained by the CAN shows American Muslims learning how to fire AK-47's and other automatic weapons, how to use rocket launchers, mortars, and explosives, and also includes instruction in kidnapping, murder, and sabotage.

Whether or not these four Muslim converts were associated with either Islamberg or Jamaat al-Fuqra, or if they were just 'freelance' terrorists is not currently known, but the proximity between Newburgh, where the terrorists were based, Riverdale, where the targeted synagogues are located, and Hancock, where the Jamaat al-Fuqra camp is located is noteworthy; Newburgh is roughly between Riverdale and Hancock. Perhaps it's a coincidence, perhaps it's not. But the mainstream media doesn't detail this kind of information; we can't even rely on the mainstream media to accurately report the facts any longer. This is overwhelmingly clear in that for the most part, the media has refused to mention that these terrorists are Muslims.

We could reasonably infer this based on their choice of target; overt Jew hatred is generally confined strictly to Muslims and Neo-Nazis, and while the former - for some reason - are simply not mentioned by the media, the latter would be harshly condemned for their 'extremist' and 'hateful' views. Not that they aren't extremist or hate filled, I was just pointing out the inconsistency in the way the media portrays evil, and noting that it is a reasonable assumption that these were Muslim terrorists. So consider the populace uninformed. As for our security infrastructure:

We should probably give both the FBI and the NYPD a pat on the back for their hard work and the innocent lives that were saved. Great job!!

What's noteworthy here is not only the law enforcement entities that were involved, but also those that were not involved. The CIA is not mentioned, and this is not unreasonable given that there has always alleged to have been some territoriality between these intel outfits. The fact that the Department of Homeland Security (DHS) wasn't mentioned, and doesn't appear to have been in on this really bothers me. The DHS, as most of us will recall, was put into place shortly after 9/11 and was chaged with the primary responsibilities of both protecting the territory of the U.S. from terrorist attacks, and to respond to natural disasters.

Where the hell was the Department of Homeland Security in all of this?

It's possible that DHS played a role in foiling this operation, and simply is not taking credit for it... maybe they were operating in a behind the scenes fashion. Probably not. It's likely being swept under the rug now, but less than 3 months ago, the DHS released a statement claiming that the chances of a homegrown terrorist attack occurring were "very low". This statement was released a few short hours following FBI director Robert Mueller's statement that his agency was "particularly concerned" about a homegrown terrorist attack.

"We are not immune to an attack from a home-grown terrorist, but the probabilities and sustainability of such an act are very low," said DHS spokesman Michael Keegan. That assessment came just hours after FBI Director Robert Mueller said his agency is "particularly concerned" that young men living in the United States could be recruited to attack the very country they call home.

Of course it's no secret that the DHS has been more-or-less an ineffective, wasteful, boondoggle; indeed, since September of 2008, the US Congress estimates that the DHS has wasted about $15 billion via failed contracts, the GAO accused DHS members of more than $2 billion in credit card fraud, and the chief of DHS cyber security obtained her advanced degrees from a diploma mill. So, while the DHS was out spending your hard earned tax dollars on items to make this nation more secure such as plastic dog booties, beer-brewing kits, and iPods, the FBI was putting at least some of your tax dollars to work actually trying to catch criminals and terrorists.

Thank God, Obama hasn't replaced Robert Mueller. Perhaps the DHS was unable to thwart this particular terrorist attack, as they were too busy assessing the threat posed by anti-abortion activists and returning war veterans. A document released by the DHS entitled "Right-wing Extremism: Current Economic and Political Climate Fueling Resurgence in Radicalization and Recruitment," and dated April 7, claims "threats from white supremacist and violent anti-government groups during 2009 have been largely rhetorical and have not indicated plans to carry out violent acts..." but goes on to suggest that a declining economy, and potential new legislative restrictions on firearms coupled with "the return of military veterans facing significant challenges reintegrating into their communities could lead to the potential emergence of terrorist groups or lone wolf extremists capable of carrying out violent attacks." This document further indicated that law enforcement agencies should be on the look out for suspicious individuals who may have bumper stickers for third-party political candidates such as Ron Paul, Bob Barr and Chuck Baldwin.

So while the FBI is out solving real crimes, that involve real criminals, the DHS is busily constructing ideological fantasies that have no basis in reality. To the detriment of the security of this nation, and - one can only speculate - for the purposes of political correctness, the DHS has taken their sights off of the real threats, and the real terrorists both within this country and without, and has boldly turned those sights on you. Indeed, the DHS has prompted law enforcement officials to act on those allegations. Human Events reports the following via email:

Rosemary from Louisiana alerted "him that her brother-in-law was stopped by small town Louisiana police and detained by the roadside for half an hour. A background check was conducted to determine whether he was a member of an “extremist” group. Why? Her brother-in-law (name not disclosed for privacy) had purchased a conservative “Don’t Tread on Me” bumper sticker..."

According to this report, this individual was harassed and detained - as a consequence of DHS's backwards report regarding right wing extremism, simply for having a right-wing bumper sticker (Please see my previous blog entries: The Emergence of the Thought Police, Update: Emergence of the Thought Police, and Drudge Report Banned). In other words, the DHS has become Big Brother, and Janet Napolitano is Big Sister. And while Big Sister keeps her watchful eye over our returning military veterans, those opposed to illegal immigration, and Ron Paul supporters, the jihadists are recruiting in our prisons, training thousands of terrorists right under our noses, and carrying out assassinations, firebombings, and other assorted mayhem.

Who's better prepared in this war? Who's taking this war seriously? Who has clearly identified their enemy, and is actively struggling against them? The jihadists have, but not the DHS.

I'll say it again, Thank God for Robert Mueller and the FBI.

I would like to be able say the United States doesn't torture; I would like for the United States not to torture. However, in an insane world, perhaps occasionally, torture is not only the only sane choice, but indeed the only morally acceptable choice.

Can torture be morally acceptable? Can torture be the morally preferred choice?

Indeed it can.

Moral questions are often complex, unique, and limited or influenced by the subjective circumstances under which they are asked. Take for example the proverbial example of a terrorist who knows the location of a nuclear bomb in a major city. The authorities are aware that this person and this person alone knows the location of the bomb, and even with this amount of notice cannot evacuate the city. If they don't find the bomb within a certain amount of time, the deaths of tens of thousands, and injury of hundreds of thousands of Americans is an inevitable fact.

Under such circumstances, I can't imagine how one could argue that not torturing this person for the purposes of obtaining the bombs location be morally acceptable. How can it be?

The choice seems quite clear to me, inflict pain and suffering on one specific ill-intentioned, subhuman, Islamofascist, or allow that specific ill-intentioned, subhuman, Islamofascist to not only kill tens of thousands of individual innocent Americans - women, children, infants - but to literally torture the hundreds of thousands who are blinded, burned, poisoned, or otherwise maimed by not torturing this person, and permitting the bomb to go off seems at best morally confused, and at worst downright evil.

Of course this is strictly a hypothetical scenario, and it certainly could never demonstrated that torture actually provided useful information, or saved even one innocent American life... or can it? According to one former CIA agent, waterboarding "worked wonders":

a leader of the team that captured al Qaeda’s Abu Zubaydah, has told network news interviewers. And that water-boarding, Kiriakou has said, produced instant results: Abu Zubaydah started talking in less than 35 seconds.

It is often claimed that torture is ineffective in obtaining confessions, as people will confess to anything to simply cease being tortured.... Hell, I'd admit to being a Justin Timberlake fan to end torture. However, we weren't trying to get a confession from Zubaydah, we were trying to save American lives. According to the same source as above,

"The next day, he told his interrogator that Allah had visited him in his cell during the night and told in to cooperate...'' "From that day on, he answered every question. The threat information he provided disrupted a number of attacks, maybe dozens of attacks.''

While torture may not be effective in obtaining meaningful confessions, it apparently is useful in obtaining useful information that could save American lives. According the the LA Times, utilization of enhanced interrogation techniques (EIT) on Zubaydah not only resulted in the disrupting attacks, but provided critical information that facilitated the capture of self-proclaimed 9/11 mastermind Khalid Sheikh Mohammed (KSM). It was believed that KSM was planning more 9/11 style attacks on the US, and indeed when questioned about upcoming attacks on the US, he replied "Soon, you will know." Given KSM's alleged role in the 9/11 attacks, those words should have been taken very seriously. In addition to providing vague and ominous sounding - but entirely plausible - threats, KSM was not cooperative with his CIA interrogators.

In other words the CIA knew, or at least thought, KSM knew about future attacks, but wasn't divulging information. In other words, the CIA believed that if they didn't waterboard KSM, that innocent Americans would be slaughtered 9/11 style. From CNSNews:

According to the previously classified May 30, 2005 Justice Department memo that was released by President Barack Obama last week, the thwarted attack -- which KSM called the "Second Wave"-- planned " 'to use East Asian operatives to crash a hijacked airliner into' a building in Los Angeles."

In other words, waterboarding of KSM actually saved American lives. Though lengthy, it's worth again quoting CNSNews regarding the use of EIT, and waterboarding in particular (special emphasis added):

" ...the CIA believes that it would have been unable to obtain critical information from numerous detainees, including KSM and Abu Zubaydah, without these enhanced techniques," says the Justice Department memo. "Both KSM and Zubaydah had 'expressed their belief that the general US population was 'weak,' lacked resilience, and would be unable to 'do what was necessary' to prevent the terrorists from succeeding in their goals."

In other words, waterboarding - simulated drowning - of exactly three scumbag, Islamofascist, murderers (Remember, KSM personally beheaded Daniel Pearl) in all likelihood saved hundreds, if not thousands of innocent American lives. In my personal opinion, it's debatable whether or not waterboarding is even torture; as Ann Coulter brilliantly pointed out, we've waterboarded more reporters than we have actual terrorists. Christopher Hitchens was waterboarded; Sean Hannity offered to be waterboarded for charity. All branches of the US military's Special Forces and certain sections of of the CIA have in the past routinely waterboarded their members, though the Pentagon won't comment as to whether or not this is still SOP.

For that matter, I'd volunteer to be waterboarded, just to demonstrate my belief that waterboarding is not torture in the classic definition.

I'll not be volunteering to personally experience any of Al Qaeda's known torture methods, and I'll bet that neither will Hitchens or Hannity. In conclusion, one can imagine myriad scenarios when torture is not only justified, but is the only morally acceptable option.

There's nothing righteous, and indeed nothing good in letting thousands of innocents be tortured because the authorities either refused, or were not permitted to torture someone hellbent on murdering innocent Americans. However, one not need imagine such scenarios; there's hard evidence that waterboarding, whether you think it's torture or not, resulted in disrupting terrorist attacks, and ultimately saved innocent American lives.

For the morally confused, for those who will reduce my post, my reasoning, and my logic to a soundbite, describing me as pro-torture, I can only state this. I can live with being called "pro-torture" based on what I've written here, but you'll have to live with being labeled "pro-mass murder" based on what would likely have happened had KSM not been waterboarded.

I can live with it, can you?

I've never been fond of the term "junk DNA"; the term seems to be loaded with a staggering degree of presumption and hubris, quite possibly reflecting the omniscient attitudes all too common among some, even many scientists.

Personally, when I teach about this portion eukaryotic genomes, I not only utilize the term "non-coding" DNA, but also generally express my disdain for the term "junk DNA".

To be honest with you, I don't even believe that non-coding DNA is an adequate term. Indeed these particular regions of the genome are not translated, but that doesn't mean the DNA doesn't encode something. For example there are many regions of the genome that are transcribed, but are not translated.... that is these regions of the genome have functionality, but it occurs at the level of RNA, not at the level of protein.

It's often surprising to people who taken a few, biology courses, but believe it or not, there are many more varieties of RNA than the three commonly taught: mRNA, rRNA, and tRNA. Indeed, a wide variety of different RNA, with unique functionalities and specifities have been discovered; wikipedia has a nice list of these different RNA types. Some of these RNAs are universal while others are found in eukaryotes only, and some are found in specific cell types. However this post isn't about RNA; it's about DNA - junk DNA specifically.

Despite the fact that I've entitled this post "More Function for Junk DNA," this is actually my first post in this blog regarding junk DNA, so I'm going to add quite a bit of background information, including a brief history of junk DNA.

The term junk DNA was first coined in 1972 by Susum Ohne, an Asian-American geneticist and evolutionary biologist. Just to be fair to Ohno, the introduction of the unfortunate misnomer junk DNA was not his only contribution to science. Ohno is credited with the discovery that the Barr body present in mammalian female nuclei is in fact a condensed X chromosome. Ohno also authored the classic book Evolution by Gene Duplication, published in 1970, wherein he postulated that gene duplication plays a significant role in evolution. Ohno's law, which postulates that mammalian X chromosomes are conserved among species, is named for this specific Ohno.

What are we talking about when we say junk DNA? Loosely, the term is probably best defined as DNA for which no known function has yet been determined. There are many different regions of the genome that classify as junk DNA; indeed 95% of the human genome does not encode for protein. There is a wide variety of non-coding DNA present in eukaryotic genomes, examples include: pseudogenes, retrotransposons, microsatellites, centromeres, telomeres, introns. Admittedly, some of these regions, telomeres, centromeres, and introns in particular have known functions, but represent non-coding regions of the genome that were not historically understood. An article summary posted on ScienceDaily yesterday reports that researchers have discovered another important role for 'junk' DNA; indeed this summary reports that junk DNA plays a "central" role in the organism.

They have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow... ...transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load. "The transposons actually perform a central role for the cell," said Laura Landweber, a professor of ecology and evolutionary biology at Princeton and an author of the study. "They stitch together the genes in working form."

In other words, enzymes called transposases reorganize the genome of an organism, then when no longer needed are removed from the organism. The article reports that these transposases are passed on in the form of maternal RNAs that is briefly passed to offspring, that also provide templates to facilitate genomic rearrangement.

We can add this to the growing list of functions that have been discovered for DNA once alleged to be 'junk.' There has always been evidence that non-coding DNA was not in fact 'junk'; for example: Studies indicated that long areas of non-coding DNA were constructed of palindromic sequences and that these palindromes maintained a symmetry between opposite complementary strands. Another study that employed statistical techniques co-opted from linguistics to study non-coding DNA within genomes, reported that non-coding DNA is organized into patterns that resemble patterns observed in human languages. Large portions of the genome called heterochromatin, which in the past were thought of as junk DNA, have been reported to play a role in the inactivation of genes, and suppression of their expression. Other evidence suggests that non-coding DNA plays a critical role in regulating expression of genes during development in general, which is further affirmed in the ScienceDaily summary that prompted this blog entry.

In addition, non-coding DNA has been reported to regulate the expression of specific genes that control development of the central nervous system, the reproductive tract, and photoreceptor cells present in the eye. Functional roles have even been found for pseudogenes. Prior to 2003, there were no known functions for any pseudogenes; pseudogenes were thought to be non-fuctional relics of related functional genes that are no longer translated and expressed in the cell. Researchers inserted a fruitfly gene into a pseudogene called Makorin1-p1 in mice. It was discovered that this lineage of genetically-altered mice exhibited multi-organ failure in approximately 80% of the individuals; the researchers on this project learned that this pseudogene was expressing an RNA molecule that regulated the expression of a functional Makorin1-p1 gene. Thus we can add this example to the growing list of functions for non-coding, or what has been historically - and unfortunately - termed "junk DNA". Indeed, this growing list of functions is extremely numerous and diverse, and contrary to popular opinion - and in stark contrast to the evolutionary explanation typically employed to explain the presence of "junk DNA" - more and more it appears that non-coding DNA is a dynamic and essential component of genome functionality, not a useless relic of imperfect process of evolution.

The swine flu - for the most part - seems to have fallen off the radar of the mainstream news. There still several things about the swine flu that are not known. In particular, it is not known how severe this particular flu outbreak will be with respect to illness and death relative to other influenza viruses.

According to the WHO, disease surveillance authorities in Mexico began noticing cases of a disease initially described as a mild influenza like illness starting on March 18. The number of cases has risen steadily since then, and again, according the the WHO, there are now 10243 cases and 80 deaths in 41 countries worldwide. The large majority of these, 5469 and 6 deaths, have occurred within the United States; the second largest number of cases, 3648 and 72 deaths, have occurred within the epicenter of the disease - Mexico. That there are more cases of flu in the USA relative to Mexico, the epicenter of the disease, most probably speaks to the relative reaction of Mexico as compared to the USA.

I thought it might be noteworthy to plot the progress of the disease to illustrate this idea. Below is a semi-log plot that follows the number of flu cases, beginning on April 29, 2009, the day that WHO first began posting any meaningful data. [caption id="attachment_63" align="aligncenter" width="497" caption="Semi-log plot: Number of Flu Cases vs. Date "][/caption]

Perhaps the most noteworthy item concerning this data is the fact that the number of cases in the USA surpassed the number of cases in Mexico relatively early on in the outbreak. The disease was handled completely differently in the two countries. In the USA, very little action was taken - though some action was taken in some isolated places. For example, 858 schools were closed throughout Texas, affecting more than half a million students; a number of schools were closed throughout California, and NYC has closed at least 16 schools.

The response in Mexico has been somewhat different; Mexico reacted to the virus by closing businesses, restaurants and schools, canceled concerts and sporting events, and advised citizenry to stay indoors as much as possible for five days. This strategy - logically - is thought to be largely responsible for keeping swine flu under control and limiting spread through Mexico. In other words the Mexican response was much more logically consistent with actually controlling an outbreak than that of the USA; and the data clearly demonstrate this.

By any standard the US response to this unknown, novel, out-of-season, potential pandemic has been lackluster and nonchalant.Whether or not a less passive approach was necessary remains to be seen. The virulence of any given disease is defined by it's case fatality ratio (CFR); a higher CFR is indicative of a more virulent virus. The tricky thing is how CFR is defined. Ideally it should be defined as number of deaths, per affected individual, however how those numbers is defined is also often tricky. In any case, the CFR is the best estimate or description of a disease's virulence. Estimates for the CFR of the seasonal flu are approximately 0.1%. The 1918 Spanish Flu Pandemic has been estimated to have a CFR ranging from 2% to 20%, depending on which sources you check, but is most commonly given as 2.5%. This particular virus, depending on which statistics you look at. Considering only the number of deaths per infected individual, the USA, Mexico, and worldwide have CFR's of 0.110%, 1.97%, and 0.78% respectively.

These CFR's are likely overestimated as well; it's reasonable to assume that the actual number of cases is higher - probably significantly higher - than the reported number of cases. A certain number of persons with mild symptoms, and those - such as myself - who simply like to avoid MD's (Unfortunately, I can't avoid other Ph.D.'s, I"m surrounded by them) will not seek medical attention, and will simply go unreported. These unreported cases will lower the CFR.

These results are probably not statistically significant as of yet. Flu seasons often occur in waves; in the US, there are often two waves of flu activity, with one wave occurring in late November and lasting into January, while another wave often occurs in January, peaking in and becoming most severe in mid-February, and finally tapering off in late March.You can see this for yourself here.

A realistic CFR cannot be calculated until there is more data, and the infection has started to subside. It could be too early to say, but thus far, it doesn't appear that this strain is particularly virulent, and the number of new cases (according to my graph) seems to be tapering off. There is speculation that this virus could mutate and become more virulent, and this certainly could occur. In my opinion, this is not very likely.

Mutations can and do occur in viruses - generally more so than in complex organisms - however, the in the evolution of viruses, in general, is for them to evolve to become less virulent, not more virulent over time. Secondly, this particular strain of flu virus is no more likely to mutate than is any other flu virus, including the seasonal flu. Thus far, the data seem to indicate that the dreaded H1N1 swine flu is no more virulent than, and no more likely to cause death than the typical seasonal flu that comes and goes each year.

Prior to commenting on this article, I should preface my commentary by stating that I support the rights of homosexuals to live their lives free from laws that interfere with or otherwise inhibit them from expressing erotic feelings for whomever they are naturally inclined to be erotically attracted to. In other words, I - for the most part - support the rights of gays to be gay, act gay, and express their sexuality however they choose - provided of course, that we are referring to consenting adults.

I say "for the most part", because I do believe there are lines that even consenting adults shouldn't be crossing. Take for example the case of Armin_Meiwes. Meiwes placed an advertisement on a site called The Cannibal Cafe, stating he sought "a well-built 18 to 30-year-old to be slaughtered and then consumed". The ad was answered by Bernd Jürgen Brandes, though apparently many other people responded to the ad, but backed out. Evidence obtained from a videotape actually made by the two shows that Meiwes amputated Brandes' sexual organ, the two tried to eat the sexual organ, and Brandes was subsequently killed. Apparently, Brandes had wanted Meiwes to bite his sexual organ off; this was not successful, however Meiwes manage to burst both of Brandes' testicles by biting them.

In my opinion - and you can feel free to call me old fashioned - this crosses the line, even for consenting adults. One last thing to clear up before I move on to the article: I'll go ahead and answer the question that's on everyone's mind: Do I support changing the definition of marriage, and allowing same-sex couples to marry?

No, I do not.

I'm perfectly willing to discuss my perspective, but perhaps in another blog entry; this entry is concerned with the gay rights movement in Russia. I came across this report on Breitbart.com, where the headlines read: Moscow police violently break up gay pride rally. The second paragraph/sentence of this article states the following:

City officials had warned they would not tolerate marches or rallies supporting the rights of gays and lesbians. Activists had targeted Moscow, which was holding the finals of the Eurovision song contest on Saturday, to press their claims that Russia officially sanctions homophobia.

There's a wealth of things I could say about this sentence. Firstly, I'd like to point out that the gay rights activists were brave to stand up for their rights in the former Soviet Union. It's no secret that Russia - that is the government, the police, and for that matter many members of the general population do not in fact support the rights of gays. Many of you may recall a similar incident in 2007; a gay pride march in Moscow resulted in the beating and arrest of several gay activists including Peter Tatchell, a British gay rights campaigner. In this instance, witnesses and participants report that Moscow police did little to restrain anti-homosexual bigots from attacking protesters.

Tatchell, who had a black eye after being punched during the march on Sunday, said police failed to intervene as marchers were attacked by nationalists shouting "death to homosexuals." Police have denied ignoring the attacks. "The behavior of the Moscow police was some of the worst I've ever experienced," Tatchell told Reuters in an interview outside a Moscow police station where he filed a complaint about the assault on him. "The police stood back and allowed the fascist thugs to attack us. They made very few efforts to stop them."

The Moscow Police deny this, stating that they in fact protected citizens to the best of their ability:

A Moscow police official, who did not want to be identified, said officers had detained many of the assailants and pulled gay rights activists to safety when they were attacked. "As far as they were able, and depending on the situation as it developed, the police ensured the safety of citizens regardless of their political and other interests," the official said.

In either case, it should be very clear - crystal, in fact that Moscow has little tolerance for homosexuals, and is not prepared to allow their marches and protests to occur. This is highlighted quite nicely by the Mayor Moscow:

Moscow Mayor Yuri Luzhkov, who has called gay marches "satanic", refused permission to hold the parade.

In this particular protest, dozens were detained, including two members of European Parliament. It should be no surprise then to the activists in this more recent example that gay rights are not going to be tolerated in the Soviet Union. The Moscow officials - as I've pointed out above - have made it perfectly clear that they would not tolerate any such protests or demonstrations by the homosexual community. I'll post that paragraph again just to make it clear:

City officials had warned they would not tolerate marches or rallies supporting the rights of gays and lesbians. Activists had targeted Moscow, which was holding the finals of the Eurovision song contest on Saturday, to press their claims that Russia officially sanctions homophobia.

The irony here is that the gay activists do recognize what's happening, they even state it; "Russion officially sanctions homophobia". I don't know that I'd call it homophobia, but in any case Russia DOES NOT support the rights of homosexuals in any capacity, and as I pointed out before the Mayor of Moscow called homosexual behavior "Satanic". What exactly did these activists expect then? At the center of these activities again, is the aforementioned activist, Peter Tatchell:

Among those detained were British activist Peter Tatchell and American activist Andy Thayer of Chicago, co-founder of the Gay Liberation Network. Tatchell and most of the others were detained during a hastily organized protest near Moscow State University in southwest Moscow, where about 30 protesters shouted "Homophobia is a disgrace of this country!" and "We are demanding equal rights!" "This shows the Russian people are not free!" Tatchell yelled as he was being dragged to a police car. He was released a short time later.

I've added special emphasis to an important statement by Tatchell, and how this right to freely assemble and protest indicates that Russians are not free?

Stop the presses!!! The Russians aren't free?!?

No kidding, Peter. Where have you been for the past ninety years or so? Ever heard of Stalin? The Gulags? Solzhenitsyn? You may want to read up on your Russian history, prior to engaging in unwelcome protests in authoritarian regimes. Just a suggestion... take it or not. Tatchell's naivete about with whom he is dealing is painfully evident in the next passage:

"The arrests were done in a very violent, aggressive manner," Tatchell told The Associated Press after his release. "We believe the reaction of the Moscow police was totally unjustified." Tatchell said Russian gay rights leaders had appealed to Eurovision contestants to denounce the police crackdown from the stage at tonight's competition. The live contest, which pits singers from different nations against each other, has drawn up to 100 million television viewers previously and is Europe's most prestigious pop song competition. "Today's arrests go against the principles of Eurovision, which are about peace, harmony, cooperation and unity between all the peoples in Europe," he said. "Gay people are part of Europe, they are part of Russia—their rights and freedoms are as important as everyone else's.

Why would Tatchell, who's been manhandled and mistreated by the Moscow police on prior occasions expect anything different this time around - especially after being specifically told his demonstration would not be tolerated. And even more absurdly, what makes Tatchell believe that the powers that be in Moscow are concerned with the opinions of 100 million television viewers? What sort of threat does 100 people sitting on their butts, watching a talent show pose to the Moscow regime? Why should the powers that be in Moscow feel threatened by these 100 million people? When have the powers that be in Russia demonstrated an overwhelming concern for the rights and privileges of their citizenry - homosexual or not? Again, Moscow has never been anything but unapologetically blunt with respect to their position on homosexuality, and protests concerned with gay rights:

"(Gay pride events) not only destroy moral foundations of our society, but also purposefully provoke disturbances that will threaten the lives and safety of Moscow residents and guests," City Hall spokesman Sergei Tsoi was quoted by the ITAR-Tass news agency as saying Saturday.

The Russian Authorities aren't fond of really any protests, pro-homosexual or not apparently:

A half-dozen anti-gay rights demonstrators were also seized by police during a demonstration in Moscow's central Pushkin Square.

The point here is not whether or not I believe that homosexual rights - in the Soviet Union or not - are important. They are; homosexuals deserve the same treatment under the law as any other citizens. However, the homosexual activists in Russia are barking up the wrong tree. Russia is a society that lacks basic freedoms that we enjoy in the US. Russia is not a free society; there is no freedom of speech, no freedom of assembly, etc. The homosexual activists want Russia society and Russian Freedoms to run before they can crawl; Russian homosexual activists would be much better off, and Russian society much better served if they sought basic human freedoms, prior the freedoms for one specific minority. In short, Russian society must learn to crawl before it can run.

Perhaps the coming police state is more imminent than any of us could have believed. This will be my third post in as many days regarding the Thought Police. Please see my previous two blog entries The Emergence of the Thought Police, and the subsequent Update: Emergence of the Thought Police. The emergence of the soft totalitarian state in the country, and the rapidity with which it is occurring is startling - frightening in fact. Politico.com reports that the U.S. Attorney's office has told employees not to log on to the right-leaning news aggregator The Drudge Report. The ban was issued based on the notion that allegedly two computers have become infected by viruses associated with the Drudge Report. From the article:

In an e-mail message sent May 4, Paul Harvey, an information-technology official for the Boston office, wrote that security specialists with the U.S. Attorney's Office at the Department of Justice asked them "to reformat/reimage two computers because the user visited the drudgereport.com site." "Please avoid the Drudgereport website from the [United States Attorney's Office] computers," Harvey wrote.

A malicious code was alleged to have been contained in an ad associated with the Drudge Report. It is further alleged that the ban was not politically motivated:

Schmaler also said the request to stay off Drudge wasn't politically motivated and said it was sent only to the office in Massachusetts. She also said other popular sites were later found to have potential viruses, including ESPN.com.

It's entirely possible that Drudge did contain an ad that included some malicious code. It will be interesting to see if Drudge actually does comment on the alleged malicious ad, and what exactly the code does. I can say this. I log on to Drudge multiple times a day - admittedly, this is generally with my superior Apple computer, but I do use Windows-based computers at work, and in years of visiting Drudge have never had a single problem. Let's say there was a single problem however, let's say that the complaint is legitimate, and Drudge did accept some ad that contained malicious code. Is that single infraction - at this point two computers affected out of what I'm guessing is millions of hits each day, worthy of banning a website? Would the same thing happen if the more professionally appearing CNN accepted an ad with malicious content on a single occasion? What about personal email? Is personal email banned there? If not, why not? Personal email is the only way most computers ever get infected with a virus or other malware. Again, I'll have to suspend judgment, but it seems that the US Attorney General's office in Massachusetts is potentially succumbing to the Left's tendency to suppress free speech

It appears that my recent blog entry regarding the emergence of the thought police was quite timely. I linked to an article from Michael Savage's site this morning that details the emergence of Britain as a soft totalitarian state. From the article:

The Government is pushing ahead with legislation that will criminalise politically incorrect jokes, with a maximum punishment of up to seven years' prison. The House of Lords tried to insert a free-speech amendment, but Justice Secretary Jack Straw knocked it out. It was Straw who previously called for a redefinition of Englishness and suggested the "global baggage of empire" was linked to soccer violence by "racist and xenophobic white males". He claimed the English "propensity for violence" was used to subjugate Ireland, Scotland and Wales, and that the English as a race were "potentially very aggressive".

In addition to the reports that I've detailed in my original blog entry, several others are detailed in this article. Take the example of Robin Page, a columnist and chairman of the Countryside Restoration Trust attended a rally against the Government's anti-hunting laws in Gloucestershire in 2002, where he was quoted as saying: "If you are a black, vegetarian, Muslim, asylum-seeking, one-legged, lesbian lorry driver, I want the same rights as you." For that quip, Page was arrested, and four months later he was informed via letter that no charges would be filed, but added a caveat stating "If further evidence comes to our attention whereby your involvement is implicated, we will seek to initiate proceedings." Five years later, Page was finally able to clear his name. Perhaps the most despicable example detailed in this article is that of a 14 year old schoolgirl named Codie Stott.

Stott asked a teacher if she could sit with another group to do a science project as all the girls with her spoke only Urdu. The teacher's first response, according to Stott, was to scream at her: "It's racist, you're going to get done by the police!" Upset and terrified, the schoolgirl went outside to calm down. The teacher called the police and a few days later, presumably after officialdom had thought the matter over, she was arrested and taken to a police station, where she was fingerprinted and photographed. According to her mother, she was placed in a bare cell for 3 1/2 hours. She was questioned on suspicion of committing a racial public order offence and then released without charge. The school was said to be investigating what further action to take, not against the teacher, but against Stott. Headmaster Anthony Edkins reportedly said: "An allegation of a serious nature was made concerning a racially motivated remark. We aim to ensure a caring and tolerant attitude towards pupils of all ethnic backgrounds and will not stand for racism in any form."

Scary. More to come.

Dennis Prager is hands down my favorite talk show host; he is a superb logician, and has a preternatural ability to articulate conservative values.He is balanced, reasonable, and always respectful. His arguments are persuasive, engaging, easy to understand, and in my opinion a pleasure to hear.

Prager is a refreshing change from typical talk radio. He's not all politics, all the time, but lives up to the motto of his show, "where [they] talk about everything in life". In any case, on a recent show, Prager articulated that he's had an epiphany - he's going to dedicate the rest of his life to promoting the truly unique, special, and important elements that have made America truly exceptional.

One particular element of his quest is the advent of Prager University, a series of short, professionally made videos that articulate different elements of American or conservative values. The first of his videos - The American Trinity has been released.I certainly recommend watching, but will briefly summarize below. [youtube=http://www.youtube.com/watch?v=Nn4IH3yng4k&hl=en&fs=1] Prager's basic premise is that the American Value System, that which has made this country unique is in fact written on every coin in your pocket. The American Trinity - according to Prager - is comprised of:

1. In God We Trust
2. E Pluribus Unum
3. Liberty

This 'American Trinity' is unique to the US; no other country has ever employed these three value systems as the foundation for their society prior to or since chosen by the US. Each of these values, these traditional American values, values that shaped this country and not only permitted, but facilitated American Exceptionalism and her greatness, is under attack and ultimately be supplanted by non-Traditional values imported from secular western Europe.

In God We Trust - America was founded as a Christian nation. The Founding Fathers didn't believe that the Constitution or the Bill of Rights were the source of rights; these documents merely articulated the rights they believe were bestowed upon all men by the Creator, a.k.a - God. Indeed if rights are bestowed upon men by men, then they can be taken away by men. This was not the belief of the Founding Fathers, and is distinctly incongruent with traditional American values. In God we trust is in danger of being supplanted by secularism. Contrary to popular belief, the Constitution says nothing about separation of church and state. This comes from some of Jefferson's personal correspondence. Secularism has no source of absolute morals or values; there is no Creator to bestow such values from a secular perspective.

E Pluribus Unum - literally means "Out of Many, One." This value articulates the fact that if you move to America, no matter where you're from, you can instantly be accepted as one of us. True, American has not always lived up to that ideal, but that is the source of the value, and is in fact one of the reasons people come to America. They know when they come here, they've got an equal chance at becoming and succeeding as an American. In other words: Values are more important than blood. This was a revolutionary concept, and undid millenia of caste, tribal, or other such unalterable or inescapable social heirarchies. You can come to America and success or failure is based entirely on one's ability to succeed or fail. This American Value is under assault from multiculturalism. As stated above, the unique thing about America was the ability to come here and be American. American society flourished as a result of a 'melting pot' mentality, not from multiculturalism.

Finally, Liberty, though this value is not unique to the US, its manifestation in the US is unique. The French also use liberty as part of their trinity, but in the case of the French, liberty is offset by equality. Equality and liberty are practically mutually exclusive values. Let me state again: Equality and liberty are nearly mutually exclusive values. Liberty implies the freedom for one to succeed or fail. If one has the option of succeeding in the face of others failing, then equality doesn't truly exist. Equality certainly is articulated in the Declaration of Independence, but refers to equality of treatment under law, not equality of result. This is where the left has gotten equality confused; equality - in the US at least - has never been about equality of result, it's always been about equality of treatment under the law.

The WHO has taken the claims of Australian researcher Adrian Gibbs seriously, and investigated his claims that the H1N1 Swine flu virus was perhaps man-made, and was mistakenly released into the environment. The WHO asked a group of virologists to evaluate Gibbs claims; the group reports that there is no evidence that the strain is anything but a naturally occurring virus (Source).

"This group of scientists feels that the hypothesis does not really stand up to scrutiny," Fukuda said in Geneva, where the WHO is based. "The evidence suggests that this is a naturally occurring virus and not a laboratory-derived virus."

I spent a good deal of time looking at sequence alignments and Phylogenetic trees over the past couple of days, and there are really only two unique things about this virus. Firstly, the virus came out of Mexico, and came during what is not historically considered to be 'flu season.' The fact of the matter is that tens of thousands of people die every year from the flu, and none of us ever bat an eyelash. It's common to see deaths from the flu during flu season... not so much when it's not flu season. The second thing the struck me as bizarre is that when I BLAST the nucleotide sequences, they show up as strains that have appeared in both North America and in Europe. I speculate that this is probably what led Gibb to conclude that the virus was likely man-made.

 I'm no virologist, but I certainly understand enough about viruses to know that they do recombine all the time. I further am aware that when two different strains of a the same virus infect the same host, that recombination can and does occur. In other words the fact that the virus is comprised of genes from two strains whose origins derive from other continents is entirely unremarkable - especially given the amount of travel and intercontinental trade that occurs. All it would really take is for a European-bred pig infected with European swine flu to be brought to North America, and mixed with hogs infected with the N. American strain.

Other elements of the sequence are equally unremarkable. For the most part there is remarkable homology between Viral sequences derived from distinct locations, there are occasional single nucleotide polymorphisms, but this would certainly be expected. We would expect this for a number of reasons: Firstly influenza's genome is composed of RNA; RNA genomes are inherently more unstable when compared to DNA genomes, and mutate much more readily. Secondly influenza genomes are relatively small - about 12kB. The small size of the genome combined with the rapid replication and mutation rates of viruses means the genome is likely to accumulate these SNP's. In looking at the sequences, there are not a large number of differences between these H1N1 strains and other H1N1 strains. Gibb commented on this rate of mutation, claiming that it seemed like there was 'accelerated evolution.' I can't actually comment of the speed at which flu genomes mutate - or at least I can only comment enough to say that the mutation rates didn't seem out of order to me. However, I will say that recombination events can make determining something like the rate of evolution extremely difficult and somewhat arbitrary.

It seems that I'm in agreement with the WHO virologists as well. I'm certainly willing to suspend judgement until I've seen Gibb's analysis, and what specific details lead him to believe this is a laboratory accident, and not simply a natural recombinatory event. Incidentally, I'm not sure that there is any way to detect a difference. If a virus has been cultured and subsequently recombines in an egg in a lab, or in a host organism in the wild, the process is the same. The enzymes, the raw materials, and the pathways used to recombine the viral genomes are the same, and recombination in eggs vs. host organisms shouldn't generate notable differences.

On a final note: the Google 2009 H1N1 Flu Outbreak Map reveals some interesting things about epidemiology in action. Note that the outbreak began in Mexico and quickly spread into the US. The responses between the two countries were almost polar opposites, with Mexico taking a hardline, conservative approach to dealing with epidemic, and implementing various restrictions and forced closures. The US on the other hand took a more laisez faire approach and did nothing. As a result of these two policy differences, the number of cases in the US has surpassed the number of cases in Mexico (Source).

14 May 2009 -- As of 06:00 GMT, 14 May 2009, 33 countries have officially reported 6497 cases of influenza A(H1N1) infection. Mexico has reported 2446 laboratory confirmed human cases of infection, including 60 deaths. The United States has reported 3352 laboratory confirmed human cases, including three deaths. Canada has reported 389 laboratory confirmed human cases, including one death. Costa Rica has reported eight laboratory confirmed human cases, including one death.

As described by Orwell in his classic novel, Nineteen Eighty-Four, the Thought Police are a secret police force, charged with the task of uncovering and punishing various thoughtcrimes – that is thinking disapproved thoughts. The Thought Police utilize invasive and ubiquitous surveillance, as well as psychology to locate and eliminate those persons in a society whose thoughts challenge the status quo.

Certainly Nineteen Eighty-Four is a work of fiction, and most of us like to think that such scenarios could never take place - and certainly couldn't occur in what is commonly referred to as the free world. Unfortunately, we’re starting to see signs of emerging thoughtcrimes in the United Kingdom and here in the US. Perhaps the most recent and most egregious of these is appropriate as it includes both of these nations; this event is of course the recent banning of radio talk show host Michael Savage from entering the UK.

Home Secretary Jacqui Smith said she decided to make public the names of 16 people banned since October so others could better understand what sort of behavior Britain was not prepared to tolerate… “This is someone who has fallen into the category of fomenting hatred, of such extreme views and expressing them in such a way that it is actually likely to cause inter-community tension or even violence if that person were allowed into the country," Ms Smith told BBC Breakfast.

Huh? Michael Savage?

Has Ms Smith ever heard Savage’s show? Have the UK’s values strayed so far from those of the US, as to seem practically alien to our sentiments?

In an effort to be entirely transparent, I must disclose that I like Savage’s show. I podcast it every day, and very rarely miss a day.

You may not like Savage; you may find his views inflammatory and disagreeable, but to claim that Savage foments hatred, or is likely to cause inter-community violence, is so far off base, that it could’ve come from The Onion. I challenge anyone to point out any statements of Savage’s that foment hatred, or could incite violence.

You can’t do it.

Perhaps Savage is an isolated case. How about the case of Sam Brown? Brown, a 21 year old Oxford University Student was arrested for – foolishly – asking a police officer “Excuse me, do you realize your horse is gay?" Brown was charged with making “homophobic comments,” it was stated that Brown’s remarks were likely to cause harassment, alarm or distress, and that his “homophobic comments that were deemed offensive to people passing by."

Read that paragraph again.

Though I could spend hours analyzing that particular snippet, I’ll just mention the major issues that pop into my head immediately. Firstly, what exactly is homophobic about referring to the officer’s horse as “gay.”? What is homophobic about that statement? Which passersby deemed the comments offensive? How many passersby? How long before the officer arrested Brown after the comment (how much of an opportunity was there for the injured parties to report this intolerable offense?)

How about the example of Samina Malik; Malik was the first woman convicted under new terrorism legislation in the UK after writing violent jihadist poems. Excerpts from Malik’s poems include classic jingles such as: "Let us make jihad/ Move to the front line/ To chop chop head of kuffar swine."

Brilliant... and it rhymes too.

And who can forget the poignant ode to decapitation "It's not as messy or as hard as some may think/ It's all about the flow of the wrist," Malik's mellifluous musings climax with the imaginative "No doubt that the punk will twitch and scream/ But ignore the donkey's a--/ And continue to slice back and forth/ You'll feel the knife hit the wind and food pipe/ But don't stop/ Continue with all your might."

Now…. I think that Malik is a subhuman… a piece of garbage, and a waste of resources, but has she committed a crime?

According to the UK she has.

How about here, in the US…. Such flagrant disregard for freedom of speech couldn’t happen here in the US, right? Think again. Evidence that not only can thoughtcrimes happen here, but are in fact already in place, and affecting Americans is right in front of our eyes… if only we’d see it. Consider the case of Beauty Pageant contestant Carrie Prejean. Ms. Prejean was asked a politically charged question, and provided an honest, if albeit controversial answer to the question of whether or not she thought gay marriage should be legalized in more states. Prejean responded with the following:

“Well I think it's great that Americans are able to choose one way or the other. We live in a land where you can choose same-sex marriage or opposite marriage. You know what, in my country, in my family, I do believe that marriage should be between a man and a woman, no offense to anybody out there. But that's how I was raised and I believe that it should be between a man and a woman."

Did Perez Hilton want her answer or not? Apparently not, because the media onslaught to discredit, embarrass, and otherwise hurt this woman was without precedent. The rant on MSNBC by Musto and Olbermann was a new low – even for MSNBC… and for what? Because she had the audacity to state what her values, her religion, and her upbringing would naturally lead her to say. Of course none of this occurred within a court of law. Perhaps you missed this (Source):

[T]he U.S. House voted 249-175 today to create a new class of crimes based on the traits of the victim, including "sexual orientation" and "gender identity…" Under the "hate-crimes" legislation, pastors could be prosecuted for preaching the biblical view of homosexuality. Similar laws have been used to prosecute religious speech in the U.S. and abroad. Rep. Steve King, R-Iowa, hosted a special meeting last night to highlight the dangers and concerns related to the bill. "Under this legislation, justice will no longer be equal," he said before the meeting. "Instead, justice will depend on the … protected status of the victim, setting up different penalties for the same crime.

This bill is reminiscent of the case of Pastor Aka Green in Sweden. Green was jailed and charged with a "hate" crime for preaching the biblical perspective on homosexuality. Green’s case didn’t occur in the US however… but wait. Somehow you missed this on CNN (source WND):

Eleven Christians who were demonstrating at a public homosexual-rights event in Philadelphia have been arrested and charged – they say unjustly….. Eight charges were filed against the protesters, including three felonies and five misdemeanors. The charges were: criminal conspiracy, possession of instruments of crime, reckless endangerment of another person, ethnic intimidation, riot, failure to disperse, disorderly conduct, and obstructing highways. The "ethnic intimidation" charge, explains Robert Knight, writing for Concerned Women for America's Culture and Family Institute, was made possible by Pennsylvania's Ethnic Intimidation and Institutional Vandalism Act – that state's "hate crimes" law – to which the newest "victim" category of "sexual orientation" was recently added.

Not only can it happen in the US, it appears that it is happening in the US. Keep in mind the words of Winston Smith from Nineteen Eighty-Four: "Thoughtcrime does not entail death: thoughtcrime is death."

In an article published on line today, it is reported that the World Health Organization (WHO) is investigating a claim that the swine flu virus may have resulted from human error.

Adrian Gibbs... intends to publish a report suggesting the new strain may have accidentally evolved in eggs scientists use to grow viruses and drugmakers use to make vaccines. Gibbs said he came to his conclusion as part of an effort to trace the virus's origins by analyzing its genetic blueprint. "One of the simplest explanations is that it's a laboratory escape," Gibbs said in an interview with Bloomberg Television today. "But there are lots of others."

There certainly are lots of others, the first thing that popped into my mind was the idea that this was an engineered virus. After all there are several peculiarities; for example, I've analyzed the DNA sequences myself, and they are from strains found in both North America and Europe. The article furthers this point:

Gibbs said his research found the rate of genetic mutation in the new virus was about three times faster than that of the most closely related viruses found in pigs, suggesting it evolved outside of swine.

So far, so good, right? Mmmmm.... I'm not so sure, if you keep reading in the article you eventually read the following:

Gibbs said he has no evidence that the swine-derived virus was a deliberate, man-made product. "I don't think it could be a malignant thing," he said. "It's much more likely that some random thing has put these two viruses together."

I've italicized the important text in the above quote: "he has no evidence" and doesn't "think it could be a malignant thing" Why the hell not? Something that can be done unintentionally in the laboratory can certainly be accomplished with intention. What evidence does he have that the virus isn't deliberately man made? How could he tell the difference? If the recombination were simply performed by mixing viruses together in eggs and isolating out particular strains there is not really any way that you could tell the difference.

An important question about this: If one chooses to speculate that the virus came from passage in eggs by vaccine development and viral production - and this point is disputed by other researchers in this article - where specifically in Mexico are these activities occuring? Is Mexico a hotbed of vaccine production? To be honest with you, I have no clue. However, if you're going to propose something such as this, you should look at the epidemiological data also. You should determine, as near as is possible, where the outbreak initiated, and whether or not there are any plausible places that such a passage may have occured. If you can't find such an institution, then - in my opinion - this increases the probability that this is in fact a deliberate engineering and release of virus into a population; in other words a bioterrorist event. In any case, I'll continue to monitor the situation, and perhaps perform some sequence analysis of my own.