Non Sequiturs

By Michael Hawkins

~Who cares what Tiger does in his sex life? He’s good at a sport. That’s why I like him.

~Why do people listen to Glenn Beck? He’s wrong about pretty much everything.

~The Tea Party is the most ridiculous, haphazard mess since, well, the Bush Administration. I guess it hasn’t been that long.

~Obama has not earned the title “Socialist” yet. I hope he one day lives up to it.

~Time Warner is an awful company.

~So is Hannaford.

~Dogs clearly are better than cats.

~Remember Mystery Science Theater 3000? That was awesome.

~And Mr. Wizard? That was good times.

~The Caps are going to win it all this year. Damn it.

~ This is the last edition of Without Apology for some time. Maybe it will be back in the fall.

~It’s okay to weep.

~Mexican food really is awful. Just awful.

~What happened to Scrubs? Why would ABC ruin something that was once so great?

~The original aerial-view GTA was pretty awesome.

~Listen, Papi, we appreciate all you did, but that was so long ago. We don’t want to boo you, so please just hit the ball.

~And can it be said? Can it finally be said? As much as Manny would dog it down the line, Papi did, too. If anything, Papi did – and does – it far more than Manny.

~Baseball needs a serious salary cap.

~Evolution is true. Deal with it.

~Start watching Holmes on Homes.

~I wake up every day and thank my lucky stars I’m not from Mississippi.
~Of course, I don’t have lucky stars, though, because astrology is a bunch of malarkey.

~Oh, heck, I’ll mention him. Christopher Maloney is a quack.

~The best part of the Kennebec Journal is the comics.

~Except Mark Trail. Everyone HATES Mark Trail.

~Hiking is great.

~Despite popular belief, “Without Apology” does not reference a refusal to literally apologize for some given mistake. It actually refers to not qualifying every little statement with unnecessary pedantry. Nuance is okay. Not pedantry.

~Swimming across the pond at Bicentennial Park will get you “banned for life”. Trust me.

Mitochondria and Microsatellites

By Michael Hawkins

Mitochondrial DNA (mtDNA) is useful for determining the phylogeny, or relationships, between closely related species. It is inherited, generally, only from mother to offspring, so it doesn’t face problems such as recombination since it isn’t recombining with other DNA before being passed on (except through horizontal transfer, or “genetic swapping” between bacteria).

One recent discovery using mtDNA has found that a sort of “pre-human” was walking around while humans and Neanderthals were still rocking out. Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany and his colleagues wrote in the journal Nature that they had sequenced mtDNA from a fossil discovered in a Siberian cave. Results showed that the former owner of those long dead bones had diverged from humans and Neanderthals a million years ago. (Human and Neanderthals then diverged 500,000 years later.)

The authors go on to state that more research is needed to determine just where the species qualitatively sits on the evolutionary tree. The point, however, is that mtDNA has proved useful in this analysis, giving a tentative quantitative determination and a tentative qualitative indication.

This is all in stark contrast to microsatellites. These are short tandem repeats, or units of repeating DNA sequences. For example, CACACACACACACACACACA is commonly seen throughout eukaryotes and the chloroplastic genomes of plants (usually every few thousand base pairs). They are generally neutral.

Microsatellites have relatively high mutational rates for a variety of reasons. Whereas in mitochondria the mutational rate can partially be chalked up to the fact that mitochondria is bacterial in origin, microsatellites have polymerase slippage to thank, or bad DNA replication, let’s say. Other studies suggest unequal crossing-over. At any rate, this mutation rate lends itself to population studies using microsatellites.

By using microsatellites as genetic markers, it is possible to determine genetic variation within a population. This works for investigating both temporal and spatial population structure, two important factors in management and conservation of species. For instance, Lage et al. 2004 looked at Atlantic cod populations ranging across Browns Bank, Georges Bank, and Nantucket Shoals.

At the time of the research, the Gulf of Maine cod were treated as a separate stock from the Nantucket Shoals and Georges Bank Atlantic cod. Browns Bank cod were even more separate as a stock since they are in Canadian waters. Using microsatellites, the researchers found Nantucket Shoals cod to have a distinct population structure from those on Georges Bank and Browns Bank, which were genetically similar. One likely reason is due to currents which keep Georges Bank cod on Georges Bank as well as somewhat rare currents which likely transport larvae from Browns Bank over the Fundian Channel (which adult cod are unlikely to traverse since they are ground-huggers and the channel is deep and cold). The conclusion is that the health of Atlantic cod populations might be better served by treating them as separate stocks based upon the discovered genetic variation, instead of the current method of utilizing particular geographical lines which may not reflect all population ‘barriers’.

The shortcoming, however, with microsatellites is that they are not useful for deep phylogenetic analysis. Their high mutation rate makes them virtually useless after a few thousand generations; they are good for pedigrees and population structure analysis, but they do not offer insights into distant relationships. Occasionally they may remain the same or nearly the same over long periods of time, but the rhyme and reason probably has nothing to do with the microsatellites themselves. Instead, they likely are located near a site of selection on a locus, thus conserving them for longer than just those few thousand generations.

Lage CR, Kuhn K, Kornfield I. (2004) Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. Fishery Bulletin, 102:289-297.

Play a Fair Game, Goodell

This article had a few words cut off the end. It is unclear what those words should have been, so that final sentence has been cut from this version.

By Michael Hawkins

The No Fun League is a pretty terribly run organization. It’s certainly an excellent business, but it’s pretty crap as far as quality sporting goes. From the tinker bell Roughing the Passer rule to the 6 required flags per play, the games are sometimes difficult to watch. It’s still a great sport and I’m not about to abandon my patriots, but c’mon. The rules make it a little onerous to enjoy at times.

The worst rule, perhaps, is for overtime (OT). The team that wins the coin toss gets to win the game. Not literally, of course, but it may as well be that way. It’s sudden death, so it’s a matter of moving down the field within 45ish yards of a field goal and booting that through. If they make it, the game’s over. It’s inane. I mean, hell, a game of beer pong even allows for rebuttal (depending on house rules; check with your local party animal for details).

What the NFL needs to do is play a full 15 minutes in OT. Make it a real game; make it a fair game. They won’t be that sensible, but a new rule has been proposed.

The competition committee recommended…to the 32 owners that a team losing the coin toss and then surrendering a field goal on the first possession should have a series of its own in OT. Such a rules change would need 24 votes for ratification.

This is still fundamentally unfair since it only applies to field goals. The first team to get the ball still has a huge advantage because if it scores a touchdown, the other team has no offensive reply. This is effectively half a football game: one offense, one defense. Goodell et al are making progress, but they’re being jackasses about it. They aren’t managing the superior sport of hockey where the beginning to any period is fundamentally fair. They’re dealing with a different scenario, a different sport, and they need to realize that. If they play a full 15, the coin toss becomes less relevant; all sports should reject embracing the role of chance. Let it come on its own.

And hell, if they want to copy the NHL so much, take a man away for the OT quarter. That’s probably a terrible idea, but 1) it would be hilarious to see the league contend with such a radical change and 2) it would be better than giving the game away to the team that happens to win the coin toss.

Field of Dreams

By Michael Hawkins

When in discussions and/or debates with the religious, I cringe before I bring up the point that, yes, of course atheism does lack a certain sort of comfort. Afterall, do people really have no fear of death? But this does not mean that fear ought to motivate one to believe in any sort of god or afterlife. An emotion, no matter how strong, does not make something true. And, frankly, it’s bizarre that anyone would ever try to make that sort of argument. But alas, I’ve encountered it a number of times.

The reason, however, I cringe is that as soon as a lack of a certain comfort is admitted, the theist jumps up and proclaims, “Aha! So you do desire a god/an afterlife!” But this isn’t so. I certainly do not desire to live with the redneck described in the Bible. But what’s really perplexing is how illogical the theist’s whole point is. “You desire X, thus X is true.” Or sometimes with some condescension, “You desire X, so maybe you ought to reflect on that a little more.” The assumptions there are that 1) I haven’t reflected on these sort of issues and 2) all it takes is reflection on a desire to come to believe in a god. The first assumption is obviously wrong and the second shows the theist’s ignorance: I want evidence, not a belief motivated by fear.

Honestly. The logical argument is that people have fear and seek to soothe that feeling; religion makes sense in light of this fact (though it needs far more than that to explain it). The theist, however, then tries to turn logic on its head and say that fear is somehow a sensation put in place by some religion’s god and that’s why we feel it. Such shenanigans completely circumvent the whole giving-evidence-for-one’s-beliefs thing – it is such a nuisance for believers, after all.

The whole crazy argument is a Field of Dreams sort of fantasy: If you desire it, truth will come.

The Absolute Reasonableness of Absolute Uncertainty

By Michael Hawkins

One of the common complaints raised by theists comes from the phrase “There’s probably no God” as one way to describe atheistic thought. This runs counter to the caricatures of atheists out there that says atheism automatically equals absolute certainty that no gods exist. To many it sounds more like agnosticism and doesn’t quite fit into their notion of what an atheism actually believes (or, rather, doesn’t believe).

In The God Delusion, Richard Dawkins actually spends more time than should be necessary on the point of how to define atheism. He creates a 7 point scale where a “1” is an absolute believer, someone with no doubt in the existence of God, and a “7” is the polar opposite, an absolutely certain atheist. In the middle are varying levels of belief or disbelief. Dawkins places himself as a “6”, describing himself as nearly certain there are no gods, but allowing for their possibility, however slim that may be. This is how a huge swath of atheists also describe themselves. (It’s at the root of some of the messages being put out on the atheist bus campaigns around the world, in fact.)

The complaint to this is the belief that atheism means absolute certainty. What requires this? The word means “without theism”. That does not imply certainty of what is true, but rather a degree of certainty of what is not true. In modern connotations, the term includes a rejection of deism and usually anything supernatural. But, still, how does this rise to become certainty?

Many people, for whatever reason, insist that any lack of certainty thus equals agnosticism. There are two issues with this. First, no, it doesn’t. Atheism, again, does not require certainty. Second, the only way one can arrive at this conclusion is to use the modern connotations of atheism. The problem comes when the connotations of agnosticism are then ignored, ever so conveniently. That is, the fact that atheism is usually taken to mean a complete rejection of all things supernatural is employed, but then the fact that agnosticism is usually taken to mean a 50/50 uncertainty is ignored. This is why Dawkins needed his scale. Few people are right in the middle (“4”). Most people lean one way or the other. In fact, it has to be hoped a majority of people do not categorize themselves as “1”, pretending as if they’re absolutely certain of their God’s existence. Everyone should have doubt; the lack of it is a mark of fundamentalism.

In essence, the argument that atheism is absolute certainty is a blatantly dishonest one. If the term means absolute certainty, then it cannot be ignored that agnosticism usually means a perfect middle ground. It is bad form to ground an argument in cherry-picked connotations; in this case, demanding a self-proclaimed atheist call himself “agnostic” due to a lack of 100% certainty is weak because the common notion of a 50/50 split for agnostics is being ignored – clearly the self-proclaimed atheist is not 50/50 on the existence of gods, no matter what label one wishes to use. This would be like demanding that anyone who says unicorns are possible must also believe the mythical beasts have a 50/50 shot of existing. Of course unicorns are possible – and everyone should acknowledge that fact – but they are exceedingly unlikely and for that reason no one believes in them. And more importantly, there is not a shred of evidence for their existence. This does not make anyone agnostic towards unicorns except in the strictest, most semantic, most useless sense.

Importantly, this goes beyond a mere game of semantics. Anyone who has bothered to debate religion with an atheist present knows full well that any show of uncertainty will gladden the heart of any nearby theist. This should not be so. The ability to say “Yes, I might be wrong” and “No, I cannot be positive” is an admirable one. (And, in fact, more theists recognize this than are likely being given credit here.)

But more germane to the issue is that any scientifically inclined atheist is an atheist based upon the availability of evidence – and there is no evidence for any god. Anywhere. Ever. There’s faith – the very antithesis of evidence – and there are (very) vaguely internally consistent texts written by the few elite, literate farmers mulling around thousands of years ago, but there is no evidence. It is on that point that the atheist mind turns. Of course (!) there is the possibility of evidence for gods. No reasonable atheist is going to deny that. The problem is just that no one has been able to produce any of it yet. Without evidence, it is unreasonable to declare knowledge on a subject; equally, it is unreasonable to declare certainty even with evidence. (And that needs some parsing.)

There are two sorts of certainty: there’s the philosophical and then there’s the practical. The philosophical is where the atheist (and hopefully the more reasonable theist) allows for a lack of certainty. There’s just no way to know some things, is there? But the practical is where the term atheism, even with a number of its modern connotations, comes in. There is as much evidence for gods as there is for celestial teapots, but no one is about to declare themselves uncertain about the non-existence of floating cookware in space. It would be impractical and nonsensical.

Let’s do away with these old canards and caricatures and move forward with a mutual and honest understanding.

March-April Edition

The March-April edition is finally here. Some extra details on it can be read here.

Thanks to Matt and Katy for contributing.

Help Take Down Naturopathy

By Michael Hawkins

There usually is no central theme to Without Apology. This is premised on the notion that a broad band of ideas is the most fruitful method of reaching people. However, sometimes there are more pressing issues.

It may have been noticed that a number of articles are devoted toward discussing naturopathy – the belief in a magical “vital force” which is central to the body being able to heal itself. At first glance this belief may seem harmless, but reality shows otherwise.

Naturopaths are licensed as a certain type of doctor in the state of Maine. This is a mistake. It would be inappropriate to go to one of these individuals for medical care. (Indeed, one of the health methods of some naturopaths is iridology; this is where one looks at the color patterns and other characteristics of the iris to make determinations about certain aspects of a patient’s health.) The low qualifications needed to become a naturopath, the sub-standard medical training, and the plainly silly diagnostic methods give the very real possibility of a naturopath prescribing contra-indicated drugs. At the very least, a waste of time and money is highly likely.

It is important to the health and safety of all Maine citizens that naturopaths lose their right to practice medicine in Maine. We ought to hold our medical professionals to higher standards.

Please email your state senator about this. Actually do it. It only takes a minute – http://www.maine.gov/legis/senate/senators/email/maillst.htm

If you do not know your state senator, email Libby Mitchell – http://www.mainesenate.org/mitchell/email.htm

The health of the gullible, the ignorant, and the simply deluded is at serious risk right now in Maine because of the status of naturopaths. It is paramount that everyone do what he or she can to prevent dangers in the healthcare industry. Write your representative and ask that Maine become the third state to have an outright ban on the practice of naturopathy.

How Naturopathy Could Kill Suzie Q

By Michael Hawkins

The following is a letter the Kennebec Journal will apparently not print. Trying to discover the reason and rationality behind the decision is futile. It’s just a bad paper.

Let’s pretend Suzie Q has a pain in her stomach. At first she chalks it up to something she ate. But the pain keeps returning. Maybe it’s a bug, she thinks.

After the pain persists for some time, Suzie Q wonders if maybe it’s stress. She slows things down for a little while.

But it doesn’t help.

Soon she decides she needs to see someone about this. She goes to a naturopath.

The naturopath assesses Suzie Q’s state. Maybe he utilizes Chinese medical astrology. ASTROLOGY. After all, accredited naturopathic schools really do teach it.

He decides Suzie Q needs garlic or some similar herbal remedy. Then he asks for his $80-200 fee.

Suzie Q goes home happy, but the pain soon deflates her again. She continues to see her naturopath, trying multiple herbs.

Six months pass when she finds herself in a hospital bed. She’s surrounded by medical doctors. Her oncologist tells her she has an aggressive stomach cancer that has progressed too far for treatment. If only she had seen him six months earlier, she might have had a chance.

What if Suzie Q was your friend? Your mother, your sister, your brother, your father, your spouse, your child? You?

Contact your representative and demand that naturopaths lose all licensing and practicing rights NOW.

The Streisand Effect

By Michael Hawkins

“The Streisand Effect” is a phenomenon named after the actions of Barbara Streisand. In 2003, she sued a website for hosting an aerial picture of her mansion, citing privacy concerns. She lost not only the suit, but even more of her privacy. The website found itself with 400,000+ hits over the next month. In short, attempts at censorship on the Internet are often met with higher publicity for the censored person, video, or picture. It is important to keep that in mind while reading the rest of this article.

Andreas Moritz is a quack from South Carolina who despises all good medical advice, acts against the well being of the sick, and preys on the vulnerable.

On his website, http://www.ener-chi.com, Moritz claims “Cancer does not kill a person afflicted with it! What kills a cancer patient is not the tumor, but the numerous reasons behind cell mutation and tumor growth. These root causes should be the focus of every cancer treatment, yet most oncologists typically ignore them. Constant conflicts, guilt and shame, for example, can easily paralyze the body’s most basic functions, and lead to the growth of a cancerous tumor.”

This is pure crackpot talk. The man has no education in oncology or basic biology and is outright dangerous. That’s why he tried to get my website, http://www.forthesakeofscience.wordpress.com, shut down.

It began May 24, 2009. I made a post titled “Andreas Moritz is a stupid, dangerous man”. In it I quote from an article written by Moritz in which he repeats much of the above anti-scientific, stupid, dangerous garbage above. He blames the victim, advocates against standard treatments, and is, well, stupid and dangerous.

Moritz soon responded, repeating his crackpot claims and demanding respect. As someone who actually likes science, I demanded evidence first. He had none.

Eventually, Moritz posted a nearly 10,000 word spam article of his (which, for some strange reason, ended with an anti-vaccine rant) and scuttled off. I presumed this was the last of my direct contact with this crackpot.

Soon my post started to show up as the number 2 result in Google for “Andreas Moritz”. The pleasure I took in this, however, was cut short February 17.

On that day, my hosting site, WordPress, suspended and blocked my website. The reason has to do with local naturopathic quack, Christopher Maloney.

Two weeks earlier I got a notice which suspended my posting rights for several days. After WordPress made me contact them (because telling me directly obviously doesn’t make sense, right?), I was informed they had received a notice which said Christopher Maloney was an actual doctor. This ran counter to a post I had where I stated precisely the opposite. They told me to edit or delete the post.

Since Maloney is a naturopathic doctor under Maine law, I corrected my post to state that he is only a doctor by a low set of standards and that the medical community rejects his status as legitimate. This apparently wasn’t good enough, hence the eventual block.

I quickly contacted PZ Myers of the blog Pharyngula, one of the largest science blogs on the Internet. He publicized my case, titling a post “Christopher Maloney is a quack”.

But it was soon discovered that Maloney was claiming to not be the one who contacted WordPress, counter to my assumption. As it turned out, Moritz would later send me an email where he bragged of his accomplishment – while also threatening “an expensive lawsuit”.

That was a mistake.

Myers soon had a post titled “Andreas Moritz is a cancer quack”. The story spread across the Internet, finding its way on to Richard Dawkins’ site, http://www.richarddawkins.net, and making the rounds through the rest of the blogosphere and Twitter. I was famous on the Internet.

It soon became apparent that Maloney and Moritz had been in contact prior to all this. That means Maloney’s claim of not being responsible for getting my site shut down is disingenuous at the very least. He shoulders the anti-science burden as much as the cancer quack.

After 6 days of the Internet tearing the two quacks apart, WordPress found its spine and returned my site. My post is again number two – but now there are far more sites which tell their readers of the quackery of Andreas Moritz. Oh, and do search “Christopher Maloney Maine”, sans the quotation marks, on both Google and YouTube.

Whatever pettiness may seemingly be apparent in all this is really a genuine, deep disdain for anti-scientific quacks. Maloney offers treatments which are ineffective, poorly evidenced, and not supported by the scientific community. His danger is passive in that what he offers does no direct harm, but it does do harm when it delays real treatments for real health issues. A person with stage 1 stomach cancer may see Maloney for an undiagnosed pain, only to be ‘treated’ with some useless herbal remedy. The cancer will continue on its path, ignoring the ineffective naturopathic ‘treatments’. By the time a real medical doctor makes a correct diagnosis, it may be too late. Why so many states, including Maine, allow people to this to other people is a mystery.

Moritz, on the other hand, is the lowest of the low. He preys upon the sick for monetary gain, offering actively dangerous advice. He blames the victim, incoherently babbles malarkey about real medical science, and tells people to forego real treatments. The disdain for this man should be high among all people, whether he got their blogs shutdown or not.

Naturopaths Are Not Doctors

By Michael Hawkins

Okay, maybe that headline isn’t entirely accurate.

Naturopaths are people who practice an alternative form of medicine which has little to no basis in reality. Under Maine law, they are actually considered doctors. They aren’t medical doctors, mind you. No, no. Maine law holds them to a lower standard, meaning they are Naturopathic Doctors (ND), not MD’s. This also gives them fewer rights than real doctors. Be thankful.

Naturopathy is a belief that the body can heal itself via its “vital force”. This is entirely magical thinking which has no basis in science, is contradicted by everything in chemistry and biochemistry, and has never had any significant research done in its favor.

One local naturopathic ‘doctor’, Christopher Maloney, wrote a letter to the editor of the Kennebec Journal several months ago. In it he espoused several untruths, verging into flat out lies. This is common practice for these sort of people, so it isn’t surprising. What was especially unfortunate, though, was that the KJ ran an extra blurb explaining that naturopaths are considered to be a certain type of doctor under Maine state law. This was entirely unnecessary and, if one is to use the standards of the medical community at large, dangerous because it gives undue gravitas to a field where relatively little medical training is actually required.

One of the dangerous things Maloney told readers was that the flu vaccine only provides 6 to 15 percent protection. He misconstrued some basic statistics. In reality (and according to the CDC), the flu vaccine offers upwards of a 90% reduction in becoming infected with the flu for healthy adults. And even in the instances where someone still gets the flu after being vaccinated, the virus is much less intense.

The reason Maloney and other naturopaths want the public to believe these things is that they are generally hyper-skeptical of vaccinations (just like Jenny McCarthy). While a faux-sympathetic tone towards vaccines is sometimes taken by these people, they actually seek to raise significant doubt; it’s one of their most obvious goals. Of course, ask them to supply any evidence to the general danger of vaccines and, well, “evidence” may well need to be defined for these people.

For instance, a review of Maloney’s site, http://www.maloneymedical.com, shows a section on autism and vaccines where Maloney offers several links to a single anecdotal story (which isn’t convincing on its own merits anyway). He ends with several other links, the most prominent of which may be his own personal anecdote.

This is not evidence.

Deepening the hole into which he placed his anti-scientific letter, Maloney goes on to state that the flu vaccine has no effect on deadly complications for any population group. What he doesn’t say is that the non-mountebank truth is that they reduce hospitalization in the elderly by 50-60% (CDC). Death rate falls by 80% (CDC).

Next – and this one really irked me – Maloney tells readers that black elderberry has been shown to “block” H1N1. The worst thing about this blatant falsehood was just how easy it was to find out the truth. PubMed features two peer-reviewed studies on this. Both (by largely the same group) show that black elderberry had some positive effects for the regular flu, but the study size was small and thus more research needs to be done. (In other words, no respected member of the medical field would ever start making recommendations on such a miniscule sample of evidence.) At no point in the paper was it indicated that black elderberry has any sort of vaccination properties (either for H1N1 or what it was actually studying – the regular flu), which is what Maloney seems to imply.

It’s because of this sort of malarkey that naturopaths are not generally considered doctors within the medical community at large. Maine law must change to reflect this fact.