Why quacks should be more cautious

One of the hallmarks of quacks is that they’re willing to latch on to any bit of science that shows even the most remote, most distant promise. One familiar quack did this for a preliminary study not too long ago. And other quacks do it all the time. They hear about some result which indicates some positive benefit from something – usually a berry or herb – and they go nuts. Forget that they reject just about everything else science has to tell us. If it fits into their paradigm, it must be true.

But of course they’re jumping the gun. Again and again a study will come out which shows promise for some substance that will help in the fight against this or that disease, but once a few more groups start taking a look, things fizzle out. Often studies will even get to the clinical stage, only to turn out to be failures. (“Failures” in the sense of not working, not in terms of science.) Companies usually are decent at protecting themselves from getting that deep if there is no benefit to be had, but they aren’t perfect.

I go on about this because I am currently reading a review article about the protein p53. It is a protein which is involved in tumor suppression. When it mutates, usually by missense mutation, it becomes involved in tumor growth by virtue of loss of function, though evidence strongly suggests that it also confers a gain of function in terms of cancer growth. I’ve written about other tumor suppressing proteins here.

I had to stop when I got to a section about post-translational modifications of the protein:

Post-translational modifications of p53 such as phosphorylation, acetylation or sumoylation have been shown to be essential in determining and regulating p53 activity in vitro. However, their effects in vivo remain difficult to assess. Sabapathy (S1) generated a ‘knock-in’ mouse strain replacing the serine 312 residue, equivalent to the human serine 315, by alanine (S312A) to abolish phosphorylation. This residue has been proposed to have a role in the regulation of p53 protein stability. p53S312A/S312A knock-in mice are viable, fertile and not –pre-disposed to spontaneous tumor formation. In addition, the p53S312A protein was found to be activated as efficiently as wild-type p53 and its turnover rate was not affected, suggesting that despite in vitro evidence this phosphorylation event may not be critical for in vivo suppressive functions.

Let’s get some of the terms out of the way. “Phosphorylation”, “acetylation”, and “sumoylation” all refer to the addition of certain chemical groups (such as phosphates) to the protein – it’s basically attaching stuff to p53. “In vitro” pretty much refers to the testing of cells in a test tube (or Petri dish, or whathaveyou) whereas “in vivo” refers to testing done on whole organisms. “Sabapathy” is a person, not a biological term. “Knock-in” refers to a type of genetic engineering. “Wild type” means the default protein, or the protein as it “normally” would appear, unmutated. (I’ve always found the term counter-intuitive.)

Now, presuming anyone is still with me here, the important aspect of the above excerpt is where it says, “In addition, the p53S312A protein was found to be activated as efficiently as wild-type p53 and its turnover rate was not affected, suggesting that despite in vitro evidence this phosphorylation event may not be critical for in vivo suppressive functions.” In other words, the genetically altered ‘test tube’ results showed that the addition of a chemical group was important, but further evidence showed otherwise. One thing this means, as all scientists know, is that we ought not jump the gun.

Another way to think of these results is to compare red hots dogs and apples. Each one is known to contain nitrites, which is a chemical compound linked to cancer. However, whereas red hot dogs have a small connection to tumor development, apples have no connection. Why? There is a complex interaction between meat and nitrites which results in the production of the actual carcinogenic compound. Apples, on the other hand, even if they did interact with other chemicals (probably ones within the body), have components which would help the immune system and thus help prevent cancer, at least to some degree. Or to use another comparison, tobacco cigarettes and marijuana contain a ton of carcinogens, but only one (cigarettes) has a causative link to cancer. Presumably some other chemical(s) in marijuana counteracts the carcinogens. But however the cancer is prevented, it happens through a complex interaction that needs to be studied. Lab results are wonderful and they’re a major reason why we live so healthy and so long today, but they aren’t the final word. In fact, we ought not think of anything within biology as being the final word. We have large scale statistical results that will be true in virtually all cases, but there are no hard and fast rules for how organisms will interact with their environments. We need to test and test and test – and science will always do that – but the real solution here is that we need to be sure we aren’t jumping the gun. After all, no one wants to be a quack.

Possibly good news for “Are You Afraid of the Dark?” fans

I’ve just read from the AYAOTD Facebook fan page that TeenNick may be adding Are You Afraid of the Dark? to its lineup in addition to all the other 90’s shows it has been airing.

I’ve yet to watch any of these (I’m not sure I even get TeenNick), but I am interested in getting a little nostalgic.

Donate to East Africa

One of the young clients where I work was in the office earlier tonight when he noticed a link to an article up on the Yahoo! News homepage. It was about a man from Somalia and the hardships he faced while fleeing from famine, so I clicked it and let him read a little bit about it. (He’s from the general area, though not Somalia specifically.) Then it got me looking for things on my own later and I found this:

Yahoo! News spoke to a reporter who is in Somalia and has seen first-hand what it’s like in the refugee camps of the war-torn and famished country.

“There was no food, no help. There are kids dying left and right—I’m not exaggerating. They buried 12 on the day I visited,” said Jason Straziuso, a reporter for the Associated Press.

“The most touching thing so far has been when this small child waved at me yesterday. I stuck my head in her tent and she was lying, motionless, flies flying everywhere and she sort of stuck her head up and waved at me,” he said. “That put a lump in my throat because I don’t know that she’s going to get better, in fact I think she has a good chance of not getting better.”

African Union forces have launched an offensive to keep aid agencies safe as they bring food and supplies to the thousands of refugees in Mogadishu.

We can’t donate to all the awful tragedies around the world, but this strikes me as one of those instances where because it isn’t a sudden event like a tsunami or an Earthquake, it can easily be overlooked. That’s why I’ve used this link to donate a little money.

Feel free to do the same, if you wish.

How to fix Facebook chat

Update: The link below doesn’t seem to do anything. This link can remedy the issue of seeing people on your chat who aren’t even online.

Since it seems that every company in the world wants to make minor tweaks to their programs, there are always little annoyances that crop up. And as everyone has known for a little while now, the latest annoyance is Facebook’s awful chat function. Here are the issues:

  • It takes up 87% of the screen
  • It pops up with one click, but no longer takes one click to minimize
  • It shows random people who aren’t even online
  • It combines chat messages with inbox messages

Solution? Greasemonkey. Presuming you are aware it is not 1998, it will revert the FB chat function back to most of its old self for Firefox and Chrome users. If you are an IE user, you probably don’t know what Facebook is and you may want to consider suicide. Or at least stop (double) clicking ads because you think someone has sent you a message.

Anyway. Greasemonkey. Install, close your browser, open it back up, voila.

Thought of the day

Listen, BlackBerry Facebook Mobile, I appreciate that this most recent update is a real update that has actually vastly improve things, but seriously, stop adding my number to my profile every time something changes. If I have deleted my number the past 6 times you updated, then why would things change this 7th time?

Come on.

Apparently basic logic is too difficult for Billo

Bill O’Reilly doesn’t believe that the Norway shooter Breivik is a Christian:

On Monday night’s show, O’Reilly was outraged that The New York Times described Breivik as a “Christian extremist” in a page-one headline, declaring that being an “anti-Muslim bigot” is what drove him, “not Jesus, not being baptized.” O’Reilly went on to assert that this was part of “a movement in the American media to diminish and marginalize the Christian philosophy.” Later in the show, O’Reilly said the Times’ headline was done to “give jihadists quarter or something like that, diminish the threat of them,” asserting that “the liberal media is so protective of extreme Islam, when it hates the left. … At The New York Times, they would all be hung.”

This one really shouldn’t be that hard. Just admit that Breivik is a self-identified Christian, but qualify that acknowledgement of the truth with the observation that he does not represent mainstream Christianity. I mean, in terms of in-group mentality he does, but in terms of action, no, he certainly does not. That should be good enough. No one is going to start thinking that, oh, I guess all Christians like to kill innocent people.

But no. O’Reilly can’t be that honest. He has to pretend that Breivik was somehow not motivated by his faith because labeling him both a Christian and an extremist would make him seem like all those icky brown towel wearing people. And I can understand O’Reilly’s motivations here. Many Americans, including Papa Bear himself, do look at Muslims with an unjustified eye of suspicion. They do this because of the publicity given to a few of their acts, not to mention the simple fact that they represent an out-group. Most Americans are Christians, and all religions encourage a negative view of anyone who is different. So yeah, it makes sense for O’Reilly to hold the view he does. It isn’t honest, but it makes sense.

O’Reilly continued his obsession on Tuesday’s show during a segment with The Washington Post’s Sally Quinn. As Quinn pointed out that Breivik called himself a Christian, invoked the name of Jesus and discussed the nature of his faith, O’Reilly insisted that “there’s no evidence that ties this guy to Christianity,” dismissing Breivik’s self-description by claiming that “Mussolini called himself a Christian.”

Uh-huh. There’s no evidence. Except for that evidence.

But O’Reilly wasn’t done. He went on to invoke the “No True Scotsman” fallacy (as others have), essentially claiming that Breivik couldn’t be a Christian because “they’re nonviolent.” When Quinn noted that most Muslims would not consider accused Fort Hood shooter Nidal Malik Hasan a Muslim, O’Reilly objected: “I’m not saying he was a good Muslim. I’m saying that he was a Muslim terrorist because he carried a business card that said ‘Soldier of Allah,’ and he committed his crimes in the name of Allah.” He added, “The guy in Fort Hood, he was acting in the name of his religion. He killed because he believed that Allah told him to kill. The guy in Norway didn’t kill because he thinks Jesus wanted him to kill those people. Jesus had nothing to do with it. He wasn’t even cited. And using the word ‘Christian’ to label this guy is dishonest.”

Right, Billo, it’s everyone else who is being dishonest here. Everyone else is taking these two exact same situations – violent acts of highly-publicized murder motivated by a heap of crazy and a dash of religion – and twisting them around. Why can’t everyone see how dissimilar they are?!

This is as bad as all those dishonest Christians who claim Hitler believed in evolution. We know he was a Christian creationist who was raised Catholic and constantly professed a belief in Jesus and God. That doesn’t particularly indict Christianity. We have plenty of other things that do the trick. For example, blatant dishonesty.

Messing with the background

I’m messing around with the background a bit. Right now I have a picture from Lake Champlain, but since the lighthouse is blocked by all the other stuff on the page, I may change it soon. Let me know here if you see something you like.

Here’s the full picture.

Renowned academics talk about God

This is fantastic.

via PZ

Swan Lake

Club 27

I know “Club 27” is a popular concept amongst music fans. It’s basically a reference to the really big, important artists out there who have died at age 27: Brian Jones, Jimi Hendrix, Janis Joplin, Jim Morrison, and Kurt Cobain. There are others, but those are the most notable. (Kurt Cobain was even been reported as talking about his desire to join the club a year or so before he actually did.)

But come on. Amy Winehouse, no matter what one thinks of her music, has not had the impact of any of those other musicians. Each one was integral to the advance of music, and a lack of mention of any one of them in a talk about the history of music is a mistake. That is not the case with Winehouse. She’s technically a member of the club because she was 27, but she does not meet the point of the meme “Club 27”: impact.