How not to do science

Via Mano, we get to learn what it was like working in the stem cell lab of Piero Anversa.

The day to day operation of the lab was conducted under a severe information embargo. The lab had Piero Anversa at the head with group leaders Annarosa Leri, Jan Kajstura and Marcello Rota immediately supervising experimentation. Below that was a group of around 25 instructors, research fellows, graduate students and technicians. Information flowed one way, which was up, and conversation between working groups was generally discouraged and often forbidden.

Raw data left one’s hands, went to the immediate superior (one of the three named above) and the next time it was seen would be in a manuscript or grant. What happened to that data in the intervening period is unclear.

A side effect of this information embargo was the limitation of the average worker to determine what was really going on in a research project. It would also effectively limit the ability of an average worker to make allegations regarding specific data/experiments, a requirement for a formal investigation.

The general game plan of the lab was to use two methods to control the workforce: Reward those who would play along and create a general environment of fear for everyone else. The incentive was upward mobility within the lab should you stick to message. As ridiculous as it sounds to the average academic scientist, I was personally promised money and fame should I continue to perform the type of work they desired there. There was also the draw of financial security/job stability that comes with working in a very well-funded lab.

On the other hand, I am not overstating when I say that there was a pervasive feeling of fear in the laboratory. Although individually-tailored stated and unstated threats were present for lab members, the plight of many of us who were international fellows was especially harrowing. Many were technically and educationally underqualified compared to what might be considered average research fellows in the United States. Many also originated in Italy where Dr. Anversa continues to wield considerable influence over biomedical research.

Wow. I was sure lucky. When I was in grad school, I was in a research group of about the same size, with primarily 3 people running 3 labs: Chuck Kimmel, Monte Westerfield, and Judith Eisen. They were independent and co-equal. Their post-docs and grad students and undergrads pretty much had free run of all of the labs, to the point where it was often difficult to tell who was officially associated with which lab. We had weekly lab meetings in which we’d freely share data with each other; if someone had a good idea or a set of relevant skills, we’d have collaborations. When it was time to publish a paper, the people who had done the work would get together to write it, and authorship reflected the research team, not some hierarchy…so I emerged from grad school with papers published with both Monte and Judith, but not a one with my titular lab head’s name on it, because he had these scruples about not putting his name on work to which he had not personally and directly contributed.

I thought that was how everyone did science, as an open and egalitarian process. I guess I was wrong.

If you want more examples of science being done badly, Harvard has released the full report on the Marc Hauser scientific misconduct case. It’s clear that he faked data, and demanded that his students confirm his hypotheses. Hauser’s defense: “people in his laboratory conspired against him, due to academic rivalry and disgruntlement”, a claim that did not hold up in the investigation.

I seriously cannot imagine Chuck Kimmel, or any of my academic mentors, ever tolerating any of the shenanigans Hauser was pulling. Just the idea that you’d gather data and then pass it up a hierarchy for analysis, and be told by your advisor what it meant…bizarre.

Man, was I lucky. I hope all of you who are in grad school are following these scandals, and seeing modeled how science should not operate — and are standing up for scientific integrity in your own labs. Be involved in every step of an experiment, collaborate and share ideas, question authority. It’s the only way to do good science.

Multi-component, schmulti-component

I’m having a light dinner while traveling off to a visit with Humanists of Minnesota, and I thought I’d deal with a little email. I got a request to address a fairly common creationist argument–here’s the relevant part of the claim.

As a member of the Greater Manchester Humanists I was recently involved in a discussion with the Ahmadi sect of Islam with regards to evolution. They had asked me to look at a couple of chapters in a book entitled ‘Revelation, Rationality, Knowledge and Truth by their prophet Mirza Tahir Ahmad. One of those chapters was called ‘The Blind Watchmaker who is also Deaf and Dumb’ – riffing badly on Dawkins’s book, of course. Suffice it to say, there was very little of any of that in the book, but during the discussion one of their number said he did not believe in neo-Darwinism because he could not see ‘how all the supporting and connecting mult-component systems could all have evolved as, for example, the eye, as it progressed through geological time.’

He quoted the hagfish and work done by Prof Trevor Lamb to show ‘just how complex those multi-component systems are’ – but when I looked up Lamb’s work it is quite obvious that he is a supporter of evolution, and that he in no way suggests that such complexity is divine in nature….!

Yep, he’s got us. If evolution were sequential, linear, and goal-directed, this would be a serious problem. If you’re used to imagining that the only way complexity can possibly emerge is by purposeful, serial action to build an end result, rather like putting together your furniture from Ikea or building a model airplane, then gosh, it all seems so impossible.

Unfortunately for the follower of Mirza Tahir Ahmad, none of that is true, and this is just a variant of the “it’s too complicated to evolve” argument, with more sciencey sounding words and references to misinterpreted fragments of the scientific literature.

Let’s consider the major misconceptions in the question.

  • Evolution isn’s sequential. It’s massively parallel. Massively. Humans have about 20,000 genes, and all of them are evolving at once, with trial runs in about 7 billion individuals. New variants are arising all the time, and then they’re tested to destruction in multiple combinations over time. Scrap your weird idea that the pieces of a complex system must be developed one at a time — they can’t, and all of them are being constantly tinkered with. It is the most badly designed scientific experiment or engineering program ever, with no controls and every variable getting randomly tweaked at random intervals. So don’t be surprised that multiple elements are getting juggled.

  • Evolution doesn’t care how it arrives at a solution — all that matters is the final effect on the organism. In the case of the eye, the viable end result is an organ with sufficient resolution and contrast, and various special purpose detectors for things like motion or looming. The organism doesn’t know or care how that comes about — it is born with a combination of attributes, and lives or dies by their success. It may have accomplished its end by, for instance, refining the lens, or fine-tuning the receptor, or building in secondary signal processing elements…or all of the above and more. The organism doesn’t care and doesn’t have any control. And in a massively parallel system, probably every level is being tinkered with, and the final solution is going to be multi-component. It would be weird if it wasn’t.

  • Evolution is not teleological. An organ like the eye is not being assembled to a set of specific, detailed instructions — it just has to work, or the organism is at a disadvantage to other organisms with better eyes. So a hodge-podge of solutions is accumulated, and the end result has all kinds of complexity. But you don’t get to argue after the fact that the details imply some specificity of purpose.

    For example, here’s a number: 343767. It’s kind of big, you might be tempted to argue that it’s a fancier or more complex number than, say, 300000 (you’d be wrong), or you might want to argue for the significance of individual digits, or find a pattern in it. Humans tend to do that. But the reality is that I just went to a random number service and asked for a 6 digit number. Similarly, eyes wandered through a random space constrained by functional requirements and ended up at a somewhat arbitrarily complex configuration — and different lineages followed different paths.

OK, that’s my off-the-cuff explanation scribbled up while I nibble on a fruit salad at a cafe in Minneapolis. The whole multi-component problem is a red herring contrived by inadequate minds that can’t see beyond their preconceptions.

Good news!

The reason we get so much resistance within the atheist community is that atheism is changing.

More and more, the strongest atheist voices are talking about nonbelief less as an end in itself, but as part of a larger conversation about social justice. It could hardly be any other way: atheism is growing not only in numbers, but in diversity. When Dawkins, Harris and Hitchens were at their most prominent, a frequent (and credible) criticism was that the faces of atheism were all white, male and affluent. To make the same claim now is to deliberately ignore some of the most vital atheist and skeptic voices that have emerged in the last 10 years.

Read the whole thing — I’m happy to see that several of the “most vital atheist and skeptic voices” are right here at Freethoughtblogs.

Dear Mr Atheist allow me to destroy evolution in 3 minutes!

That’s the title of a video I was sent that is supposed to utterly crush my faith in evolution. By the way, why is it that people who worship faith as a perfectly valid way of knowing so insistently insist that evolution is wrong because it takes too much faith to believe in it? Shouldn’t that be a sign to them that it’s even better than God?

I don’t know why anyone is impressed. It’s an ignoramus ranting at his cell phone camera, reciting tired, familiar creationist tropes.

evolution is not a science…because it was never observed…which is why it is called a theory.

But people have observed and documented evolution, and done experiments to test its predictions, gone out in the field and the lab to do science guided by the theory. Of course it’s a science! And it’s called a theory because it’s predictions have been successfully tested, and the mechanism has a lot of useful properties to inform the science. I don’t think he knows what “theory” actually means, but if you stuck it out to the end, you know his grasp of language is rather weak.

Then he blathers on with creationist misconceptions about evolution. We developed different characteristics because we willed it? “Will” doesn’t play any role in evolutionary theory. And of course he has to trot out Creationist Thermodynamics, which he defines as chaos can never produce order…because it defies the logic and laws of science, which is not something the laws of thermodynamics claim, and naturally he has to babble about tornado in a junkyard. Thanks, Fred Hoyle, your legacy lives on!

Then he wraps it all up with made-up etymology. You know what universe means, right? Uni, one; verse, like in a poem. Therefore Uni-verse means one single spoken statement, just like the book of Genesis says. Too bad the dictionary says otherwise:

late Middle English: from Old French univers or Latin universum, neuter of universus ‘combined into one, whole,’ from uni- ‘one’ + versus ‘turned’ (past participle of vertere ).

As long as we’re making up word origins, I think it’s clear that it’s like “united” + “versus”, meaning “everyone against”, reflecting the inimical, conflict-driven nature of existence, and therefore we have to all gather and laugh at the dumb-ass obnoxious mouth-breather who made that video.

No cure for insomnia here

I’m not adjusted to Pacific time yet, so I woke up this morning at 3am, and figured the thing to do is watch some boring debate…and you may have heard that Sye Ten Bruggencate debated Matt Dillahunty last weekend. Just the thing! Bruggencate is a tedious kook, and it’s just the thing to put me to sleep.

But then it turns out that Bruggencate’s position is so far out there it jarred me constantly. He’s arguing that belief in god is reasonable, and here’s his reasoning:

Why is it reasonable to believe god exists? Because it is true that god exists.

I say it’s true that god exists, therefore it is true that god exists.

You can’t know what’s ultimately real without revelation from god.

This is called begging the question. His entire opening argument is snippets of video of Matt Dillahunty, quotemined bits that he falsely boils down to claim Dillahunty is a solipsist who can’t tell whether he’s a brain in a vat.

And then, darn it, Matt is a really good debater and drills right down to Bruggencate’s fallacious approach. I keep saying this, that debating is a very specific skill, scientists don’t do debate, and you need someone who knows both sides inside and out. It was very entertaining to watch Bruggencate publicly dissected. Too entertaining. How am I going to get back to sleep?

So I kept going, and Bruggencate is infuriatingly obtuse. Also not conducive to sleep.

So here you go, better than a quart of coffee.

Evidences presupposes truth, truth presupposes god.

Grrr. Idiocy. And ultimately he admits that he regards Scripture as Absolute Truth.

I’ve debated Jerry Bergman, and I thought that was a futile exercise with a fool. I would not be able to calmly argue with Bruggencate, so kudos to Matt.

Oh, and a suggestion for Matt. One of the questions in the Q&A was from a neuroscientist who questioned the value of philosophy, and asked for a specific example of a genuine contribution of philosophy to our understanding. Matt fumbled it a bit, though, but there’s a really easy answer to give to a scientist who asks that kind of dismissive question about philosophy.

Philosophy gave us science.

There’s more, obviously, but that one ought to silence any anti-philosophical scientism.

A clusterfk

In an interesting discussion of the genetic structure of human populations, Jeremy Yoder weighs in on Nicholas Wade’s little book of racism.

So with all due respct to Sewall Wright, modern genetic data pretty clearly show that if aliens arrived tomorrow and started sequencing the DNA of planet Earth, they would probably not sort Homo sapiens into multiple genetic subspecies. It is true that people from different geographic locations look different—and we have known that these visible differences have a genetic basis since the first time distant tribes met and interbred. But that interbreeding, and our drive to explore and settle the world, have maintained genetic ties among human populations all the way back to the origin of our species.

As the evolutionary anthropologist Holly Dunsworth notes in her discussion of A Troublesome Inheritance, whether you choose to focus on the visible differences among human populations, or on those deep and ancient genetic ties, comes largely down to a matter of personal inclination. Knowing what I do of evolutionary genetics, and of how our judgments about the visible differences among human populations have shifted over time, I’m far more inclined to think that the social, economic, and cultural differences among human societies are products not of our genes, but of how we treat each other.

Wade’s inclinations are, quite obviously, different from mine. However, comparing Wade’s claims to the scientific work he cites, I find it hard to conclude that we are simply looking at the same data with different perspectives. Time and again, data that refutes his arguments is not only available and widely cited in the population genetics literature—it is often in the text of the papers listed in his endnotes.

By the way, Wade has responded to various criticisms. I would not have thought he could dig himself any deeper, but he succeeded.

Despite their confident assertions that I have misrepresented the science, which I’ve been writing about for years in a major newspaper, none of these authors has any standing in statistical genetics, the relevant discipline. Raff is a postdoctoral student in genetics and anthropology. Fuentes and Marks are both anthropologists who, to judge by their webpages, do little primary research. Most of their recent publications are reviews or essays, many of them about race. Their academic reputations, not exactly outsize to begin with, might shrink substantially if their view that race had no biological basis were to be widely repudiated. Both therefore have a strong personal interest (though neither thought it worth declaring to the reader) in attempting to trash my book.

Holy crap. Nicholas Wade is a journalist who has no standing in any field of biology, and his criticism is that those who have repudiated his book aren’t experts in the very narrow and specific subfield of biology that he has deemed the only one of importance? And that they’ve only published scholarly reviews in science journals, rather than in the primary literature? You know that publishing a tertiary summary in a mass-market newspaper would have far less credibility to scientists, right, especially with Wade’s penchant for getting the science wrong?

Getting a Ph.D. is only the start of a scientific career — scientists spend their whole lives learning and exploring new ideas (that’s why it’s a little weird to see people getting multiple Ph.D.s — it’s really not necessary. Once you’ve got one, you’ve got the tools to be a scholar.) My grad school advisor started out his career with a degree in immunology, and drifted towards neuroscience, and then development, and then genetics as his career progressed — it would be really weird to judge his work as just an immunologist.

Scientists get trained in thinking scientifically more than anything else — something that Nicholas Wade missed.

Maybe it is demons

The latest explanation for schizophrenia published in a real journal:

Hallucinations are a cardinal positive symptom of schizophrenia which deserves careful study in the hope it will give information about the pathophysiology of the disorder. We thought that many so-called hallucinations in schizophrenia are really illusions related to a real environmental stimulus. One approach to this hallucination problem is to consider the possibility of a demonic world. Demons are unseen creatures that are believed to exist in all major religions and have the power to possess humans and control their body. Demonic possession can manifest with a range of bizarre behaviors which could be interpreted as a number of different psychotic disorders with delusions and hallucinations. The hallucination in schizophrenia may therefore be an illusion—a false interpretation of a real sensory image formed by demons.

This was published in the Journal of Religion and Health, so you can trust it. Unless you think religion poisons everything.

Is Ken Ham literate?

It’s an open question. He’s quite irate with me for stating the truth, which he says is a lie, while confirming that I was accurate.

One atheist blogger is claiming that I was wrong to write on Wednesday that Rachel Maddow of MSNBC TV declared that our Ark Encounter would be built using taxpayer money (through tax incentives). The blogger (PZ Myers) stated:

"He [Ken Ham] declares that no Kentucky taxpayer money is being used to construct the Ark Encounter, but that is a claim no one made. Maddow says quite clearly several times that the Ark Park has been given $43 million in tax incentives — that is, Answers in Genesis has been exempted from a requirement to pay taxes on their for-profit enterprise, and will also receive rebates on sales taxes. So all Ham has done is rebut a claim that Rachel Maddow did not make."

Well, judge for yourself. At the beginning of her mocking rant against us Maddow stated:

"And when the creationist group Answers in Genesis announced their plans to build their Noah’s Ark theme park, the state of Kentucky offered them $43 million dollars in tax incentives for them to build that theme park …".

You can hear Maddow say it for yourself at around the 1:55 mark of the video captured at https://answersingenesis.org/ministry-news/creation-museum/media-coverage/rachels-rant-msnbc/ . The atheist blogger has once again, as such secularists often do, did not tell the truth—and of course Rachel Maddow didn’t tell the truth, either.

I said, and Rachel Maddow said, that Ham received $43 million in tax incentives. We know exactly what that means: he got tax exemptions and rebates that would total $43 million as an incentive to construct his monument to idiocy. So when Ken Ham says we’re lying because no armored cars rolled up to his front door and unloaded big canvas bags with dollar signs printed on them, he is replying to a claim we did not make. Which I also clearly said in that bit of mine that he quoted.

You know, on the cop shows when a suspect is accused of X, and he immediately starts blustering “I did not do Y!”, you kind of suspect that he’s guilty of something. What is Ken Ham hiding?

Demons. It’s all demons.

Let us emulate the godly believers. We know what is right, and anything that deviates from it is…mental illness. But we might want to remember that sometimes the shoe is on the other foot.

Some people believe that atheism causes insanity.

But what about the variety of mental illness from which Richard Dawkins suffers? You see, that is the flip-side of the coin which belongs to the man on the corner who believes he is Napoleon. Dawkins may not believe he is a conquering French general, but he believes something just as preposterous. He believes that he himself does not exist. As illogical as that sounds, this is the ground which atheism is forced to defend. The worldview which insists we cannot believe (or know) anything aside from our senses is just as mentally ill as the worldview which insists that we cannot believe our senses.

Or that faith is an essential component of a mentally sound human being.

…the evidence today implies that atheism is a form of mental illness. And this is because science is showing that the human mind is hard-wired for faith: we have, as a species, evolved to believe, which is one crucial reason why believers are happier – religious people have all their faculties intact, they are fully functioning humans.

Therefore, being an atheist – lacking the vital faculty of faith – should be seen as an affliction, and a tragic deficiency: something akin to blindness. Which makes Richard Dawkins the intellectual equivalent of an amputee, furiously waving his stumps in the air, boasting that he has no hands.

Or that the root cause of what we call mental illness is an absence of god.

All Depression is caused primarily by a lack of contentment. For the Christian, depression is a lack of obedience to the command "be content with what you have". It is not accepting your current condition, whether good or bad. It is a lack of faith that God loves you. It is a lack of hope of the glories and riches of heaven awaiting. For the non-Christian, depression is a lack of faith in a creator. It is a rejecting of Jesus for faith in Darwin. Darwin said we have no purpose, design, meaning other than random chance processes. Jesus can cure the depression of the atheist because their life has meaning and eternal purpose.

That source charmingly tells us exactly what mental illness is.

The Bible clearly teaches that people suffer both physically and emotionally as a result of sinful choices. The world labels this suffering as a mental illness, but the Bible labels this suffering as the consequences of a sinful standard of morality. Mental illness is sinful conduct.

A lot of atheists seem to think that same thing: that violations of conventional mores, or doing acts that harm people, are prima facie proof of mental illness. There must be something organically wrong with their brains to cause them to engage in behaviors we don’t like. They pray? They must be crazy, that doesn’t work. At the same time, the other side is saying, “They don’t pray? They must be crazy, god must be served.” If we’re going to define mental illness as something someone judges to be bad behavior, then every single human being on the planet is crazy.

Mental illnesses are real. We can identify chemical imbalances in the brain; if you’re depressed, drugs like TCAs, MAOIs, SSRIs, and SNRIs can be effective in making people healthier. Schizophrenia is real and debilitating; there are also antipsychotic drugs that reduce the symptoms. Obsessive-compulsive disorders are real; they can be treated with certain antidepressants, but also behavioral therapy also seems to be effective in reducing the problems. We actually do have fairly concrete indicators of genuine illnesses that affect the functioning of the brain.

However, it is not helpful to categorize bad ideas as similar. Elliot Rodger was a disturbed individual, but it was not because he had a disease — it was because he had been shaped by his narrow little world to regard a host of malignant ideas as perfectly normal. Almost all Europeans and Americans once believed that black people were inferior, and used that belief to justify everything from excluding them from educational opportunities to kidnapping and slavery. Were they all insane? Or did they just have a set of false, untested beliefs that they blithely propagated from generation to generation?

One would think that atheists, at least, would be able to recognize the power of ideas to shape how people think. We live in a world where the majority give credulous credence to religious nonsense, and I think most of us recognize that it’s not a symptom of a brain disease, but of the power of socialization, indoctrination, repetition, and widespread unquestioning acceptance. If you’re willing to see that a religious idea can have such potency that people will kill and die and suffer for it, why are you unwilling to see that there are other ideologies that can misdirect minds in lethal directions? That bad stories can persuade healthy, normal people to do stupid, evil things?

I’d also like to remind my fellow atheists of another way people think.

When a 700 Club viewer asked host Pat Robertson today if she should give up proselytizing to her atheist coworker and “let her perish,” Robertson speculated that the colleague might be possessed by demons or a survivor of rape.

If the way you are using the phrase “mentally ill”, with no evidence of genuine organic illness, can be replaced freely by the word “demon-possessed” without changing the sense, then you are engaging in the same magical thinking, using a phrase with no explanatory power. You’re just using the modern materialistically correct wording to express the same old sentiment, inventing a concrete causal agent with no evidence that it actually exists. That’s something else atheists need to be aware of: the seductive power of teleological or simplistically causal thinking to the human mind.