Science journalists accept logical fallacy, therefore journalism is compatible with stupidity

I said I was done with this guy, but his latest includes a bit that annoys me to no end. Keith Kloor interviews Daniel Sarewitz to get ammo for his claim that religion and science are compatible.

Based on your piece, I would presume that you think the two are compatible. However, some of the prominent New Atheists, such as PZ Myers and Jerry Coyne, insist that science and religion are incompatible. Why has this discussion become so binary? Why the either/or mindset exhibited by some atheists?

DS: There are lots of scientists who are also religious, so as an empirical matter science and religion are apparently not incompatible.

Gah. Dumb.

There are scientists who believe the earth is 6000 years old and that there was a global flood 4000 years ago. Therefore, science and creationism are perfectly compatible.

There are accountants who skim off profits and hide them in the books, therefore accounting is compatible with criminal larceny.

There are doctors who smoke, therefore smoking is compatible with healthy lungs.

Why has this discussion become so binary? Easy. Because some scientists have gigantic religious blindspots and want to pretend that their gullibility is part of their science.

And a complementary view from Ars Technica

When I agreed that many so-called ‘controversies’ don’t warrant a debate, I wasn’t saying that we shouldn’t cover them…just that they should be addressed appropriately, as fringe issues. The last thing we would want is media silence on, for instance, creationism! Ars Technica has a good piece on why we mustn’t be quiet about weird political positions.

Through the years I have received countless e-mails and have read hundreds of article comments imploring Ars to keep "political" stuff off the site. Such entreaties most commonly occur in relation to our scientific coverage of climate change or evolution, but also when we cover biological and anthropological matters of gender and sex. (They also come to a lesser extent when we cover the inherently political world of intellectual property, where, coincidentally, there are far fewer facts—but that’s outside the scope of this editorial.)

What those petitioners do not realize is that in asking us to be silent, they require that we take a politicized stance. Intentional silence is support for the status quo, and as such, it’s inherently political. Note that I’m speaking of intentional silence or avoidance, purposely not covering a topic so as not to bring light to it. Inasmuch as our editorial mission is, in part, to cover the issues relating to science and technology that are most challenging to our culture, it is unthinkable for us not to cover these issues. To reiterate, not covering them would be just as "political" as covering them.

This is also why I ignore or mock people who complain that “The movement has been co-opted by people with an agenda” — everyone has an agenda. Demanding silence on topics you don’t like is a symptom of having an agenda.

It needs to be said

David Hone has a good piece on what constitutes an appropriate subject for debate, and how the media fails.

The truth however, is near inevitably that there is only a very small minority making a disproportionate noise about their case. There is no debate over evolution, or the dinosaurian origin of birds, or that HIV leads to AIDS, or that climate is changing, or a great many others. That there are real, accredited scientists who do not think this is the case is not in doubt (sadly). But that this represents a real schism in the scientific community, that large numbers of researchers take these positions and that it occupies a significant amount of scientific research, or that there is good evidence for that position is certainly incorrect. One or two people arguing a point (and often doing so primarily in the media) does not make a debate.

…

This for me seems like the opposite of what good journalism should be. Surely the point is to provide a representation of the true state of affairs rather than spin (even if unintentionally) the fact that there is disagreement as something that is effectively 50:50, when it’s 99.9:00.1 or less. This can be humorous from an insider’s position when one sees the media triumph a paper as ‘reigniting the debate over x’ when in truth the researchers have looked at the paper, noted an obvious flaw or that it simply rehashes old and incorrect arguments or data, and carried on. The flipside of this is where there really is a scientific debate, in which case the debate is not reignited at all, but merely still going on, it has merely come to the attention of the press and public again which is not the same thing at all.

At least I have noticed over the years a decreasing tendency for newspapers to try to couple every discovery about evolution with a quote from some creationist somewhere, so I think the situation is slowly improving.

‘Journalists’, feel some shame for your profession

So I checked the lead political story on CNN:

CNN poll: It’s a dead heat

Then I checked the lead political story on MSNBC:

NBC/WSJ poll: Very close race with one day to go

Feeling desperate, I even checked Fox News:

CLOSING TIME: In Final Hours, Are
There Still Undecideds Left to Swing?

Do you sense a theme? It’s one that we’ve suffered with for the entire election season: news media that are obsessed with the horse race rather than the issues.

Fuck the media. Only xkcd sees the truth.

And tomorrow is the race itself, with non-stop coverage of exit polls, with maps showing trends, and predictions, and declaring that one state has gone to one candidate or the other — it’s all our media live for, I think, is the ultimate orgasm of who wins, rather than the substance of the consequences of electing either of these people.

I hate them. I hate them all. I will not be watching any of those channels, I will not be visiting their websites at all tomorrow: I am going to vote and then I am going to shut out the yammering ninnies for the whole day, and I will check my newspaper for who the winner was on Wednesday. I might be nice and create an election day thread for you all here, but I will not be reading it myself.

The real election campaign is long over. We were supposed to have news that clearly discussed the differences and similarities between the two. We didn’t get that, so now we get numbers filtered out of noise.

Also, Salon’s top two articles on tomorrow’s election are all about the polls…but they also have an article by Robert Reich on Romney’s destructive policies. More of that, please. I don’t give a damn about the polls — the only one that counts is the election itself.

Arrest everyone who disagrees with me! Show trials for all!

R. Joseph Hoffman is a flaming authoritarian, about as illiberal as you can get without joining the Tea Party. He’s very, very upset at Terry Jones and that gang of blithering idiots who assembled that terrible movie slandering Muslims, provoking riots in Egypt and Libya. Oh, and also his comrades-in-arms, Jerry Coyne, Eric MacDonald, and me.

I have just one question for PZ: What are you thinking now? God save the First Amendment?

Actually, I suppose he could bothered to read what I wrote on the “work of a group of incompetent fundamentalist Christian assholes pissing on entire cultures”, but that would be too much too ask — R. Joseph Hoffman is very busy raging at the voices in his head. I don’t even know why he bothers to ask what I’m thinking, since it won’t matter what I say, what with his fantasies informing his perceptions. I mean, we went around on this before, and he interprets what I wrote as “Hoffman coddles Muslims”. Go ahead, read what I wrote; you’ll have a very tough time pulling that interpretation out of what I said.

But what do I think of this situation? May reason save the rule of law.

Terry Jones and his compatriots are idiots, but they have a right to say hateful, awful, evil things. I’d say the same is true of the Rev. Phelps, the KKK, the Catholic Church, the Mormons, and R. Joseph Hoffman. I should have the right to say how much I despise them all, and I should also have the right to tune them out and ignore them. I’d actually rather they spoke up and made their positions clear; the threats I get in email don’t trouble me so much as the worry that the ones who’ll actually do something dangerous aren’t so stupid as to open their mouths and announce their intent.

Terry Jones is an intolerant ignoramus, but I don’t worry about him. What bothers me more are the intolerant ignoramuses who riot and murder when they’re offended; I’d rather they went out and made an incompetent propaganda film, for instance. I worry that our president might actually listen when Egypt calls for world-wide censorship, as when the White House explored the idea of having an offensive video removed from youtube (Google said no, fortunately — but they do assist in local censorship efforts).

Decide that a Terry Jones must be silenced, and who is next? I can tell you: atheists. Egypt has arrested Alber Saber for the crime of atheism.

On Wednesday, September 12th, a Muslim friend and neighbor using Saber’s computer reportedly discovered that he was the admin for the Egyptian Athiests Facebook page, which is the largest of several such groups online with over a thousand “likes”. On September 10 the notorious “Innocence of Muslims” had been posted on the site. Over the next two days crowds began to gather outside his house, threatening Saber and his mother.

On Thursday night Saber’s mother called the police, hoping for protection. When the police arrived however, rather than fending the threatening mob outside, they arrested her son.

The charge according to his lawyer and supporters, focuses on videos in which Saber discusses his own Coptic faith or lack thereof. This makes sense as to charge anyone for posting the “Innocence of Muslims” video would set an impossible precedent. Even conservative broadcasters have also shown the video, or sections of it on their shows. It is not yet clear however, which materials will be included in the case against him, which is currently in the hands of the General Prosecutor. The next hearing is expected in four days.

After talking with Saber’s friends it seems likely to me that Egypt’s Islamist leaders are hoping to create a local issue where they can be seen as the tough guys, to distract Egyptians from how the furor in the international arena, in the context of which they seem impotent.

There is no difference between what the Egyptian government has done to this man, and what R. Joseph Hoffman asks the American government to do to Terry Jones:

Arrest him without delay. Deploy the National Guard. Surround the Church.

No. That’s totalitarianism. Free speech isn’t free if you’re only allowed to speak government- and church-approved opinions. It’s surprising how many people cannot comprehend that.

(via Why Evolution Is True)

Tom Holland is censored

Channel 4 in the UK made a program called “Islam: The Untold Story”, and got so many complaints and threats that they have cancelled the screening of the show. This is a disgrace: the program is a serious, historical look at Islam, and the protesters are complaining because it takes an objective look at the evidence. We must be able to scrutinize Islam. If they’re going to hide their origins in obscurity, lies, and threats, then their beliefs should be dismissed.

I haven’t seen the program (and at this rate, I never will!), but I can make an informed guess at the content. It’s presented by Tom Holland, author of In the Shadow of the Sword: The Birth of Islam and the Rise of the Global Arab Empire, an excellent and entirely sympathetic review of the history of Islam. He discusses the deep roots of Islam, formed in a culture that was shaped by its proximity to the frontier between the two great empires of the ancient world, Rome and Persia. He traces the origins of the Islamic holy book, and discovers that no, it didn’t simply appear in 7th century Arabia (although he does think there was a singular original text), but that Islamic thought coalesced long after the time of Mohammed…and he points out that there is no contemporary evidence at all of this person Mohammed — which sounds awfully familiar to those of us who are more exposed to the Jesus myth — and that there is a long history of self-deluding Islamic ‘scholarship’ that has a lot of similarity to the self-serving confabulations of Christians.

It doesn’t make negative judgments about Islam at all, unless, of course, you find reality offensive. I thought it was an excellent book to explain the complexities of Islamic history, and it made Islam more human and more interesting. It’s well worth reading.

It would also be worth watching, if Channel 4 would grow a spine. And if Channel 4 can’t manage it, I don’t know how we can ever hope to see it in the US.

Those of you living in the UK can watch it here. They block us Americans, I’m afraid.

The stupidification of all media

I saw that Doonesbury made a joke of it, so I had to look it up. It’s true. Americans were surveyed to see which presidential candidate they thought would handle a UFO invasion best.

The channel surveyed 1,114 Americans in late May to get their thoughts on all things alien in anticipation of the channel’s upcoming series "Chasing UFOs." It even asked which superhero Americans would turn to first in the event of an alien invasion. (It’s the Hulk.)

Obama was particularly strong on the issue with women, with 68% saying they favor the president when it comes to dealing with flying saucers. And 61% of male respondents agreed. Obama also did well among Americans older than 65, with fully half of those surveyed casting their lot with him.

I really don’t give a damn which candidate won, any more than I care which comic book character they think would best fight little green men.

No, what made my eyebrows rise was the perpetrator of this idiocy.

National Geographic Channel found that nearly 65% of Americans surveyed said they believed that Obama was better able to handle an alien onslaught than the Republican presidential candidate.

The National Geographic Society is not synonymous with the National Geographic Channel, which is largely owned by News Corporation, Rupert Murdoch’s sinister organization. But still…National Geographic has their good name attached to this garbage? For shame.

Why would anyone want a complete simulation, anyway?

The NY Times is touting a computer simulation of Mycoplasma genitalium, the proud possesor of the simplest known genome. It’s a rather weird article because of the combination of hype, peculiar emphases, and cluelessness about what a simulation entails, and it bugged me.

It is not a complete simulation — I don’t even know what that means. What it is is a sufficiently complex model of a real cell that it can uncover unexpected interactions between components of the genome, and that is a fine and useful thing. But as always, the first thing you should discuss in a model is the caveats and limitations, and this article does no such thing.

I’d like to know how fine-grained the model is; I get the impression it’s an approximation of interactions between molecular components based on empirically determined properties of those elements. Again, I don’t think the authors have claimed otherwise, but it’s implied by the NY Times that now we have an electronic simulation that we can plug variables into and get cures for cancer and Alzheimer’s, without ever having to dirty our hands with real cells and animals anymore.

That’s nonsense. Everything in this model has to be a product of analyses of molecules from living organisms; they certainly aren’t deriving the functions and interactions of individual proteins from sequence data and first principles. We can’t do that yet! The utility of a model like this is that it might be able to generate hypotheses: upregulating gene A leads to downregulation of gene Z, a gene distantly removed from A, in the model, and therefore we get a preliminary clue about indirect ways to modulate genes of interest. The next necessary step would be to test potential drug agents in real, living cells. This model will have a huge mountain of assumptions built into it — and you can only build further on those speculations so far before it is necessary to cross-check against reality.

Also, isn’t it a bit of a leap to jump from a single-celled, parasitic organism like M. genitalium to human cancers and brain disease? Yet there it is in the second paragraph, a great big bold exaggeration.

And then there’s the really weird stuff. Some people need to step back and learn some biology.

“Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data,” Dr. Covert wrote. “I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that.”

What the hell…? Look, I could (if I had the skills) generate an hourglass simulator that calculated the shape and bounciness and stickiness of every grain of sand, and stored the trajectory of each as they fell, and by storing enough data for each grain, generate even more than half a gigabyte of data. So? This doesn’t mean that an hourglass is a denser source of information than a cell. The storage requirements for the output of this program do not tell us “how much data a living thing truly holds” — that statement makes no sense.

As for “We often think of the DNA as the storage medium, but clearly there is more to it than that”…jebus, does a professor of bioengineering really need to go back and take some introductory cell biology courses, or what? Heh. “More to it than that.” I’m glad to see that someone needed an elaborate computer simulation to figure that out.

I am, for some reason, reminded of the time I attended a seminar by a computer scientist on an exciting new simulation of the genetic behavior of viruses that I was told would have great predictive power for epidemiology. One of the first things the speaker carefully explained to us was how they’d incorporated sexual reproduction into the model. I wish she’d waited to the end to say that, because it meant that I sat there listening to the whole hour talk with absolutely no interest in any other details.

Gotcha!

This is an account from Connie Schultz’s facebook page, so I’ll put the whole thing here for you fb-haters.

Email from conservative blogger, dated July 9, 2012:

Dear Ms. Shultz,

We are doing an expose on journalists in the elite media who socialize with elected officials they are assigned to cover. We have found numerous photos of you with Sen. Sherrod Brown. In one of them, you appear to be hugging him.

Care to comment?

An exposé! Of the elite media! And he’s got the photographic evidence! It sounds so Breitbartian. And the followup is a classic Breitbartian pratfall.

Response, dated July 10, 2012:

Dear Mr. [Name Deleted]:

I am surprised you did not find a photo of me kissing U.S. Sen. Sherrod Brown so hard he passes out from lack of oxygen. He’s really cute.

He’s also my husband.

You know that, right?

Connie Schultz.

I’m sure this will make headlines at the Drudge Report or the Daily Caller or The Blaze or some similar right-wing schlock factory.