Conservapædia must have a stiffy for me

Just the other week, Conservapædia made their page on PZ Myers their featured article for the week; now they’ve made the Pharyngula blog a target of their cranky ire. Here’s their description:

Myers’ blog is also listed by the science journal Nature, which also embraces evolutionary pseudoscience, as the best blog by a scientist. Pharyngula is known for its sarcastic and often specious criticism of creation science and intelligent design theory,[3][4] as well as regular postings of photos of cephalopods (often with vulgarly sexual connotations both subtle and blatant).

Isn’t it charming that they lump Nature and a mere blog as similar? I do appreciate that they noticed “subtle and blatant” vulgar sexual connotations about cephalopods — I’m going to have to offend them even more in the future, thanks to their encouragement.

(Remember, we have spam filters in place because Conservapædians tend to go nuttily excessive in their whining; don’t link directly to the site, and always name it as “Conservapædia” to avoid the filters.)

Ray Kurzweil does not understand the brain

There he goes again, making up nonsense and making ridiculous claims that have no relationship to reality. Ray Kurzweil must be able to spin out a good line of bafflegab, because he seems to have the tech media convinced that he’s a genius, when he’s actually just another Deepak Chopra for the computer science cognoscenti.

His latest claim is that we’ll be able to reverse engineer the human brain within a decade. By reverse engineer, he means that we’ll be able to write software that simulates all the functions of the human brain. He’s not just speculating optimistically, though: he’s building his case on such awfully bad logic that I’m surprised anyone still pays attention to that kook.

Sejnowski says he agrees with Kurzweil’s assessment that about a million lines of code may be enough to simulate the human brain.

Here’s how that math works, Kurzweil explains: The design of the brain is in the genome. The human genome has three billion base pairs or six billion bits, which is about 800 million bytes before compression, he says. Eliminating redundancies and applying loss-less compression, that information can be compressed into about 50 million bytes, according to Kurzweil.

About half of that is the brain, which comes down to 25 million bytes, or a million lines of code.

I’m very disappointed in Terence Sejnowski for going along with that nonsense.

See that sentence I put in red up there? That’s his fundamental premise, and it is utterly false. Kurzweil knows nothing about how the brain works. It’s design is not encoded in the genome: what’s in the genome is a collection of molecular tools wrapped up in bits of conditional logic, the regulatory part of the genome, that makes cells responsive to interactions with a complex environment. The brain unfolds during development, by means of essential cell:cell interactions, of which we understand only a tiny fraction. The end result is a brain that is much, much more than simply the sum of the nucleotides that encode a few thousand proteins. He has to simulate all of development from his codebase in order to generate a brain simulator, and he isn’t even aware of the magnitude of that problem.

We cannot derive the brain from the protein sequences underlying it; the sequences are insufficient, as well, because the nature of their expression is dependent on the environment and the history of a few hundred billion cells, each plugging along interdependently. We haven’t even solved the sequence-to-protein-folding problem, which is an essential first step to executing Kurzweil’s clueless algorithm. And we have absolutely no way to calculate in principle all the possible interactions and functions of a single protein with the tens of thousands of other proteins in the cell!

Let me give you a few specific examples of just how wrong Kurzweil’s calculations are. Here are a few proteins that I plucked at random from the NIH database; all play a role in the human brain.

First up is RHEB (Ras Homolog Enriched in Brain). It’s a small protein, only 184 amino acids, which Kurzweil pretends can be reduced to about 12 bytes of code in his simulation. Here’s the short description.

MTOR (FRAP1; 601231) integrates protein translation with cellular nutrient status and growth signals through its participation in 2 biochemically and functionally distinct protein complexes, MTORC1 and MTORC2. MTORC1 is sensitive to rapamycin and signals downstream to activate protein translation, whereas MTORC2 is resistant to rapamycin and signals upstream to activate AKT (see 164730). The GTPase RHEB is a proximal activator of MTORC1 and translation initiation. It has the opposite effect on MTORC2, producing inhibition of the upstream AKT pathway (Mavrakis et al., 2008).

Got that? You can’t understand RHEB until you understand how it interacts with three other proteins, and how it fits into a complex regulatory pathway. Is that trivially deducible from the structure of the protein? No. It had to be worked out operationally, by doing experiments to modulate one protein and measure what happened to others. If you read deeper into the description, you discover that the overall effect of RHEB is to modulate cell proliferation in a tightly controlled quantitative way. You aren’t going to be able to simulate a whole brain until you know precisely and in complete detail exactly how this one protein works.

And it’s not just the one. It’s all of the proteins. Here’s another: FABP7 (Fatty Acid Binding Protein 7). This one is only 132 amino acids long, so Kurzweil would compress it to 8 bytes. What does it do?

Anthony et al. (2005) identified a Cbf1 (147183)-binding site in the promoter of the mouse Blbp gene. They found that this binding site was essential for all Blbp transcription in radial glial cells during central nervous system (CNS) development. Blbp expression was also significantly reduced in the forebrains of mice lacking the Notch1 (190198) and Notch3 (600276) receptors. Anthony et al. (2005) concluded that Blbp is a CNS-specific Notch target gene and suggested that Blbp mediates some aspects of Notch signaling in radial glial cells during development.

Again, what we know of its function is experimentally determined, not calculated from the sequence. It would be wonderful to be able to take a sequence, plug it into a computer, and have it spit back a quantitative assessment of all of its interactions with other proteins, but we can’t do that, and even if we could, it wouldn’t answer all the questions we’d have about its function, because we’d also need to know the state of all of the proteins in the cell, and the state of all of the proteins in adjacent cells, and the state of global and local signaling proteins in the environment. It’s an insanely complicated situation, and Kurzweil thinks he can reduce it to a triviality.

To simplify it so a computer science guy can get it, Kurzweil has everything completely wrong. The genome is not the program; it’s the data. The program is the ontogeny of the organism, which is an emergent property of interactions between the regulatory components of the genome and the environment, which uses that data to build species-specific properties of the organism. He doesn’t even comprehend the nature of the problem, and here he is pontificating on magic solutions completely free of facts and reason.

I’ll make a prediction, too. We will not be able to plug a single unknown protein sequence into a computer and have it derive a complete description of all of its functions by 2020. Conceivably, we could replace this step with a complete, experimentally derived quantitative summary of all of the functions and interactions of every protein involved in brain development and function, but I guarantee you that won’t happen either. And that’s just the first step in building a simulation of the human brain derived from genomic data. It gets harder from there.

I’ll make one more prediction. The media will not end their infatuation with this pseudo-scientific dingbat, Kurzweil, no matter how uninformed and ridiculous his claims get.

(via Mo Constandi)

I’ve noticed an odd thing. Criticizing Ray Kurzweil brings out swarms of defenders, very few of whom demonstrate much ability to engage in critical thinking.

If you are complaining that I’ve claimed it will be impossible to build a computer with all the capabilities of the human brain, or that I’m arguing for dualism, look again. The brain is a computer of sorts, and I’m in the camp that says there is no problem in principle with replicating it artificially.

What I am saying is this:

Reverse engineering the human brain has complexities that are hugely underestimated by Kurzweil, because he demonstrates little understanding of how the brain works.

His timeline is absurd. I’m a developmental neuroscientist; I have a very good idea of the immensity of what we don’t understand about how the brain works. No one with any knowledge of the field is claiming that we’ll understand how the brain works within 10 years. And if we don’t understand all but a fraction of the functionality of the brain, that makes reverse engineering extremely difficult.

Kurzweil makes extravagant claims from an obviously extremely impoverished understanding of biology. His claim that “The design of the brain is in the genome”? That’s completely wrong. That makes him a walking talking demo of the Dunning-Kruger effect.

Most of the functions of the genome, which Kurzweil himself uses as the starting point for his analysis, are not understood. I don’t expect a brain simulator to slavishly imitate every protein, but you will need to understand how the molecules work if you’re going to reverse engineer the whole.

If you’re an acolyte of Kurzweil, you’ve been bamboozled. He’s a kook.

By the way, this story was picked up by Slashdot and Gizmodo.

Democracy leads us into a vortex of self-destruction!

We’ve been doing politics all wrong. Michael Voris has the answers. The problem with democracy is all these voters with different views on things like abortion and homosexuality, where people who vote for such things are just rotten parasites who want to destroy civilization. So he has two solutions: 1) only allow good Catholics to vote, and 2) ideally, get rid of democracy altogether and instead install a Catholic dictatorship.

Really. He says that. I’m not making it up!

By the way, If you want to know more about life in a Catholic dictatorship, read this letter from Jim Walsh. He’s being completely non-judgmental!

I want to be perfectly clear. The contents of this letter are not to be construed as judgmental but rather observations of Catholics as it pertains to Mass attendance and conduct.

From early childhood Catholics are taught of the true physical presence of Christ in the holy sacrifice of the Mass,

This letter is not a catechism lesson. As a Catholic enters the church they are expected to display the utmost respect of Christ’s presence in the tabernacle at all times not just during the Mass. The Catholic church is not just an ordinary building, it is holy ground.

The respect for the Mass, etc., has been deteriorating at a rapid pace. Disrespectful making the sign of the cross. Do not know if they are making the sign of the cross or swatting a fly.

Irreverent genuflecting or bowing before entering the pew. Using the church bulletin as a substitute for pre-Mass spiritual meditation as though they were reading the Sunday paper or at the reading room of the library.

Loud verbal socializing with their neighbor. Dress more appropriate for the beach or working in the yard, garden or I personally wouldn’t be seen taking the garbage like some dress.

Does God care? Probably not if that’s all you have to wear. Be mindful what you wear can advertise your attitude.

Remember before receiving Holy Communion a Catholic must have made his confession and fasted one hour from food products, juices, sodas, gum, mints, etc., before he may receive communion. Drinking water is permissible. If violated, one should not receive the Eucharist.

Approach to receive the Eucharist with utmost respect and reverence and with hands held in a respectful position, not in your pockets or down by your side. You’re not standing in the communion line to receive a piece of candy. If received by hand, they be sure they’re clean.

After receiving the Eucharist, return to your pew reverently, not chewing the Eucharist like a piece of candy. Kneel and reflect prayerfully on what has just taken place. Thank Him for allowing Him to come into your body.

Recite all prayers of the Mass and sing all the hymns which are prayers put to music.

Bless yourself and bow reverently at the appropriate times of Mass. If you are a cantor, lector or choir member dress appropriately. Don’t be a distraction. Many altar servers are not trained properly or in cases I’ve seen not at all. Ushers should be properly dressed and when passing the collection basket do it with respect, not like passing the hat at a sporting event.

Priests, refrain from using the pulpit for humor. If you want to be a stand-up comic go on Saturday Night Life. I don’t think Christ began his sermon on the mount with a joke.

Finally, let’s cut out the applauding. You have not just attended a rock concert or state show.

Yours for improvement and the proper respect for the Catholic Mass. Less than that is not expected, I am not judgmental but rather observant concerned practicing Catholic.

Jim Walsh

Wilkes-Barre

His message is incomplete, though. I could help him out with suggestions on how to reverentially and appropriately desecrate Jebus crackers.

Newt Gingrich on gay marriage

Newt Gingrich, the man who told his wife he was leaving her as she lay in a hospital bed sick with cancer, has declared that “overturning Prop 8 is an outrageous disrespect for our Constitution and for the majority of people of the United States who believe marriage is the union of husband and wife” on his website. Unfortunately for him, he left comments open, and is on the receiving end of a lot of contempt for his hypocrisy.

My favorite so far is “Which one of your multiple marriages was the most sacred to you?”.

I’m also rather peeved that Gingrich’s website has the url of newt.org. He has deprived some worthy member of the Salamandridae of a good and memorable web address! Not to mention the dishonor he’s already brought to the good name of the Pleurodelinae. I can’t believe that guy is mumbling about running for president again — I’d rather see a real mud puppy in the office.

From the department of not getting it

Muslims in Saudi Arabia are building a giant clock that resembles Big Ben, but is over six times larger. They want to replace Greenwich Mean Time with Mecca Time as the world standard.

As Mohammed al-Arkubi, manager of one of the hotels in the complex, put it: “Putting Mecca time in the face of Greenwich Mean Time. This is the goal.”

This is a beautiful example of cargo cult science. Big Ben has nothing to do with establishing GMT — it’s just a big clock in London. GMT is entirely about establishing a uniform standard reference time. It was set rather arbitrarily to the time at an observatory in England, because England was the leading maritime nation at the time and used solar observations relative to Greenwich to determine the longitude of ships at sea. Greenwich time has also been replaced since then by Coordinated Universal Time, which is based on measurements of a world-wide network of atomic clocks, which turn out to be more reliable than figuring out the position of the sun.

It’s an arbitrary standard, get it? Building a giant clock in the desert will not suddenly attract time to line up with it. Although it does sound like a perfectly kitschy and annoying clock, with bright lights that can be seen 18 miles away that will flash and blink in colors to let people know it is time to pray. I suspect they’re also trying to standardize the web back to 1995 html, too.

And of course there is more. There is a whole lot of freakish cargo cult science going on down there.

According to Yusuf al-Qaradawi, an Egyptian cleric known around the Muslim world for his popular television show “Sharia and Life”, Mecca has a greater claim to being the prime meridian because it is “in perfect alignment with the magnetic north.”

This claim that the holy city is a “zero magnetism zone” has won support from some Arab scientists like Abdel-Baset al-Sayyed of the Egyptian National Research Centre who says that there is no magnetic force in Mecca.

“That’s why if someone travels to Mecca or lives there, he lives longer, is healthier and is less affected by the earth’s gravity,” he said. “You get charged with energy.”

What does that even mean? The magnetic north pole is currently located somewhere near Ellesmere Island, in Canada, and it wobbles about a lot, by several miles each year. How can a city in Saudi Arabia be in perfect alignment with an island in Canada? Being at the magnetic north pole, or even aligned with it, doesn’t mean there is no magnetism there, it’s not going to change how gravity works, and it’s not going to zap you with energy.

What the Saudis clearly need to do is build a 2000 foot tall horseshoe-shaped magnet in Mecca, cover it with strobe lights and Allah’s name, and then pray for the earth’s core to rotate and drift in alignment with their little monument.

By the way, if you’re just laughing at those dumb Muslims, keep in mind that Christians look exactly the same to us atheists. Every one who thinks that the heavens proclaim their petty parochial deity’s glory…you’re just as wacky and blind as the desert misogynists throwing away their oil wealth on knick-knacks for Allah.

Relativity = relativism

That darn English language that makes words with different meanings sometimes sound similar — it always ends up confusing Christian conservatives of very little brain, whose depth of understanding can only be measured in micrometers. The latest from Conservapædia is that they are on a crusade against Einstein…because smart people who study relativity aren’t reading the Bible, and because a theory about relationship between matter and energy and the speed of light encourages people to be open-minded and tolerant about different ideas, other than the Fundamentalist Evangelical Christian Kakistocracy (FECK for short).

Andy Schlafly is a real boon to us Gnu Atheists who argue that religion rots your brain.

(Remember, “Conservapedia” is a filtered word here; use the “Conservapædia” fancy spelling to refer to it.)

I get email

I have sad news to report. John A. Davison has gone insane. No, I know, he’s been nuts for a long, long time, but I was just purging the ol’ trashed mail folder today and discovered that he has been writing to me two or three times a day, usually just by dumping his latest comment on his poor dead blog, which mainly consists of him talking to himself about how everyone is ignoring him, and isn’t joining his crusade against Richard Dawkins, Wesley Elsberry, and PZ Myers, and how we’re all terrified of JA Davison and Darwinism is going to disappear any day now to be replaced by his theory.

As I skimmed through a sampling of the 106 tirades he has sent to me this summer, I felt sorry for the poor old guy. There he is, sitting in Vermont, shaking his fist at his imaginary enemies who don’t even notice his existence until they find his missives clogging up the spam trap. He’s the most quixotic kook I’ve ever encountered.

So here you go, pathetic old man. A little sop to your ego. If you’d like, you could imagine me seething with rage and fear, pressing the button to dispatch my team of ninjas to take you out once and for all…but they all refuse, trembling with trepidation at getting JAD cooties, and citing the importance of guarding the copy of the Origin of Species in my house. I tried to send the cyborg zombie squid, but they all mentioned that Vermont is land-locked. So you’ve foiled me for now, Davison, but mark my words, someday…someday my minions will play on your lawn.

Dear Pee Zee,

gary hitch

Thank you for your support but this is not the place to give it. Nobody pays any attention to this weblog. I get an average of 20 hits per day. The place to go after these degenerates is on their own turf, Pharyngula, After The Bar Closes, Panda’s Thumb and Uncommon Descent, all venues from which this scientist is banished. I refuse to assume aliases, use suberfuge or any other device to penetrate their cowardly defenses. The only way these egomaniacal tyrants will be defeated is by a mass uprising generated by real intellectuals like yourself who have properly identified them as the danger to our society they have become.

I read their blogs and see no support for my science anywhere. Like my sources I too do not exist. We have never been allowed to exist. There is also no place for a personal God in science and the Christian right is just as guilty as the Atheist left. My name is not mentioned at any of these weblogs because the heads of those weblogs are terrified of the message that I and my sourcse have alway delivered: there is absolutely nothing in the Darwinian model that ever had anything whatsoever to do with any aspect of the ascending creative sequence that the fossil record so obviously displays.

In an earlier response I asked you to demonstrate that you have challenged our adversaries. Have you done so? Where can I find your challenges? It is nice to have another supporter but that doesn’t feed the bulldog. What is needed is a confrontation in which the enemy is forced to confront their adversaries in a public forum, something that they are loathe to do because they know they will lose. I have done everything in my power to achieve this result and I have failed. If there really are those who agree with me, where are they to be found? I can’t find them. One thing is certain. If and when they speak they must use their real names if they expect to be taken seriously by either freind or foe. Everyone knows who this investigator’s primary enemies are. They are Clinton Richard Dawkins, Paul Zachary Myers and Wesley Royce Elsberry along with their thousands of dedicated followers. Now where are those who will lend their real names to mine and demand that this conflict be resolved.

I now propose that a public confrontation be arranged between those who subscribe to the Darwinian model and those who reject that model in favor of a guided phylogeny in which chance has played a trivial role.

I present this in the form of a petition which requires that those in favor of this resolution signify their approval by submitting to me via my private mail their full name and a description such that their identity is properly revealed to be that of a real person. Which side they represent is of no consequence.

I will present those names right here. Now we will see who really wants this crisis resolved by the only means it ever will be resolved, by real people with real names, people who have real convictions that they are willing to stand by with the time honored tradition that “a man is as good as his word.”

[email protected]

I will list those names as they appear here.

John A. Davison, Professor Emeritus of Biology, University of Vermont. Mailing address: L4 Grandview Drive, South Burlington, VT 05403

Dear Professor Dawkins,

The above petition, message #260, has yet to produce a single signature. Not a soul has offered to support my suggestion that the Meyers/Elsberry/Dawkins Darwinian Triumvirate should face this critic in a public confrontation. I find such apathy appalling. It reveals an evolutionary community completely cowed by the atheist “Darwinista.” Refusing to join with me in a most reasonable request offers a tangible explanation why Darwin’s infantile dream persists. That reason in a word is APATHY.

We are dealing with a brutal intellectual tyranny whose primary goal is to remove God from every aspect of Western Civilization.

Thomas Jefferson understood the role of silence when confronted with danger –

“All tyranny needs to gain a foothold is for people of good conscience to remain silent.”

Those who remain silent support the enemy. Darwinian mysticism has gained far more than a foothold. It has come to dominate even our institutions of higher learning as I and others know from personal experience. That dominance will continue to grow unchecked until such time as an enlightened citizenry realizes what is happening to it and acts. I have offered such an opportunity in the form of the above petition. While, personally, I am bitterly disappointed, I am not surprised.

All great civilizations have ultimately failed and ours is no exception.

Sincerely,

John A. Davison, Professor Emeritus of Biology, University of Vermont. Mailing address: L4 Grandview Drive, South Burlington, VT 05403

And then I pushed the delete key and they all disappeared.

If he starts increasing the frequency of his email now, I might report back…in December. He’ll need a Christmas present, after all.

Crème de la Chick

The latest Chick tract is a wonderful summary of modern fundamentalism. It’s got all the totally non-Biblical dogma: the anti-christ will be appointed pope, the Rapture, the weirdly fabulous Wedding of Jesus with his Church (everyone gets crowns!), Armageddon, the mark of the beast…it’s all in this one. Also, raging anti-Catholicism. Cute ending, too.

i-1b708db1d3ec98b67c2c4ace90c0a8ba-chick.jpeg

After reading everything that comes before, Delores’ “He’s nuts” is just perfect. If I were in a conversation with a fundy, and he suddenly vanished in a clap of thunder, I wouldn’t freak out, though: I’d applaud.

We’ve angered another crackpot

Uh-oh. Seed Media has received some demands from Robert Lanza, MD, Scientist, Theoretician, Genius, Renegade Thinker. He wants us to take down a few posts by Orac and myself. I guess he doesn’t like being compared to Grandpa Simpson, or seeing disagreement with his ideas about the afterlife, or being exposed as a quantum woo-meister.

Gosh, what will I do?

Seed has a very clearcut policy on our posts, and there is going to be no attempt to censor any of them. Gee. So I’m not going to edit them.

I’d hate to think that anyone might link to this post, or to these presumably objectional posts #1, #2, or #3. That might increase the likelihood that Google will return those links in searches for Robert Lanza. Whatever you do, don’t link to any of these posts about Robert Lanza on Scienceblogs!

NPR is a faith-based organization

I blame Barbara Bradley Hagerty — or at least, she is the face of religious inanity at NPR. She has a new piece up titled Christian Academics Cite Hostility On Campus, and does she have any evidence for this claim? None at all. Actually, she has evidence contradicting the claim.

There are two parts to the story. The first is someone who is fast becoming a usual suspect, Elaine Howard Ecklund, the person who studied faith among academics and was surprisingly surprised to discover that, golly gee whiz, nearly half go to church! This is a fact that is only news if you’ve bought into the biased view that academics are a monolithic bunch who are not only all atheists, but are also all communists, hippies, and Democrats. How the fact that a very significant minority of academics are religious argues that Christianity is oppressed on campus is a mystery.

So she moves on to pointing out that most of the religious academics are quiet about it; there’s a serious shortage of proselytizing evangelicals on the faculty. This, too, is a mystery to Ecklund, but shouldn’t be. Academics tend to be smart people. Evangelical/Charismatic/Fundamentalist religions are stupid. Figure it out.

Ecklund is also annoying because she is constantly harping on her thesis that higher education doesn’t erode faith, when the proper way to look at her data is to notice that more than half are freethinkers.

If you thought that was feeble, wait until you see the second part. They had to go looking for an evangelical Christian who has suffered discrimination for his faith, and who did they get? Mike S. Adams. That’s the most horrendous example of religious discrimination they could find? A far right lunatic who was tenured at his university but failed in his attempt at promotion to full professor?

Come on. Once upon a time when Christians complained about persecution, it was because a few of their members were getting fed to bears or getting nailed upside down to a stick…and now they’re reduced to squeaking about a college professor not getting a promotion?