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Science Isn’t Broken? Of Course It Is!

According to FiveThirtyEight.com’s Christie Aschwanden, “Science Isn’t Broken. It’s just a hell of a lot harder than we give it credit for.” Aschwanden’s article is a remarkably clear and forceful tour of all things wrong with science—poor statistical practice, poor study design, conscious and unconscious manipulation of data, outright falsification of data, plagiarism, fraudulent peer reviews, predatory publishers, fake authors of gibberish articles in mostly fake journals, ingrained psychological biases, and over-enthusiastic journalists breathlessly reporting on each new study as if it is the Truth etched in stone. But despite all that, she concludes that:

Science isn’t broken, nor is it untrustworthy. It’s just more difficult than most of us realize. We can apply more scrutiny to study designs and require more careful statistics and analytic methods, but that’s only a partial solution. To make science more reliable, we need to adjust our expectations of it.

Aschwanden is one of my favorite science journalists, but in this case I feel like she dipped her toes into the abyss and turned back, unwilling to to take that final step into the terrifying unknown of admitting that yes,  science is broken—obviously, deeply broken. It is permeated by perverse incentives that reward publishing results over discovering truth, and corporations are hijacking scientific institutions to give their products the stamp of scientific validation. No simple fix in how journalists report about science or to the details of statistical practice or study design will fix it.…

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How likely is it that there are aliens around KIC 8462852?

Like many, I was fascinated and excited to read about KIC 8462852, “The Most Mysterious Star in Our Galaxy.” According to Ross Anderson, writing for The Atlantic, citizen scientists looking at data from the Kepler Space Telescope for signs of extrasolar planets picked out KIC 8462852 as having a very peculiar light curve. Whereas stars with orbiting planets show dips in their brightness of up to 1% as planets pass between them and our telescopes, KIC 8462852 showed dips of up to 22%:
Kepler's light curve for the entire 1580-day observation period, showing two large dips in brightness, near days 793 and 1520. Source: Boyajian et. al, "Planet Hunters X" http://arxiv.org/pdf/1509.03622v1.pdf.
Kepler’s light curve for the entire 1580-day observation period, showing two large dips in brightness, near days 793 and 1520. Source: Boyajian et. al, “Planet Hunters X” http://arxiv.org/pdf/1509.03622v1.pdf.

Tabitha Boyajian, a postdoc at Yale working with the Planet Hunters program, and her coauthors considered several possible explanations for the dips, including instrument malfunction, dust orbiting the star, contamination of the star’s light curve by nearby stars, and comets disturbed out of their usual orbits by a passing star. They found severe problems with each explanation, but settled on a comet as the most likely possibility.…

Will You Ever Be Able to Upload Your Brain? – The New York Times

The Singluarity is not so near?

Futurist Ray Kurzweil is famous for arguing that “The Singularity is near,” meaning that soon humans and machines will merge; we will be able to upload our minds to the cloud and live forever. Kenneth D. Miller, a neuroscientist at Columbia University, agrees that something like this could one day be a reality, but he doubts that it will be anytime soon:

Much of the current hope of reconstructing a functioning brain rests on connectomics: the ambition to construct a complete wiring diagram, or “connectome,” of all the synaptic connections between neurons in the mammalian brain. Unfortunately connectomics, while an important part of basic research, falls far short of the goal of reconstructing a mind, in two ways. First, we are far from constructing a connectome. The current best achievement was determining the connections in a tiny piece of brain tissue containing 1,700 synapses; the human brain has more than a hundred billion times that number of synapses. While progress is swift, no one has any realistic estimate of how long it will take to arrive at brain-size connectomes. (My wild guess: centuries.)

Miller goes on to explain all of the additional difficulties future scientists would encounter in this endeavor due to the enormous complexities of our brain’s anatomy. His argument is fascinating even if you aren’t hoping to live for eternity on Google Drive; I had no idea just how complex the components of our brain such as neurons and synapses are. Each synapse is a world in itself.

Kurzweil’s rebuttal would be that although all of these tasks appear intractable now, the exponential growth of scientific knowledge will reduce the difficulty of each problem Miller identifies far faster than the pace of current scientific progress suggests. One of Kurzweil’s favorite examples is the Human Genome Project, which took 7 years to sequence the first 1% of the humane genome and just another 7 years to sequence the last 99%. I suspect, however, that even exponential growth might not save Kurzweil in this case. After all, not all rates of exponential growth are equal and it’s not like we have full-brain “sequencing” machines just yet.

Adding complexity to our models does not necessarily give us a more realistic picture of brain circuits because we do not know enough about the details of this complexity to model it accurately, and the complexity can obscure the relationships we are trying to grasp.

That adding more detail to a model does not always increase model performance is an effect that has been well-studied in the domain of climate science. Are there philosophers studying brain modelling as well?

Source and Image: Will You Ever Be Able to Upload Your Brain? – The New York Times

The history of science has been West-centric for too long – it’s time to think global

Schaffer & Sivasundaram: The history of science has been West-centric for too long

If you’re like me, you probably give a brief nod to non-Western science in your history courses. Perhaps you discuss Arabic astronomy or Chinese clocks. And then you get back to the familiar narrative of Copernicus, Newton, and Darwin. Historians of science Simon Schaffer and Sujit Sivasundaram are trying to change that—to tell a truly “global history of science”:

“A standard tale is that modern science spread around the world from Western Europe, starting about 500 years ago based on the work of those such as Newton, Copernicus and Galileo, and then Darwin, Einstein, and so on,” explained Schaffer. “But this narrative about the globalisation of science just doesn’t work at all. It ignores a remarkable process of knowledge exchange that happened between the East and West for centuries.”

 

“Successful science is seen to be universal in its applicability,” added Sivasundaram. “Yet, accounts of scientific discovery, heroism and priority have been part and parcel of a political narrative of competitive ownership by empires, nations and civilisations. To tease this story apart, we focus on the exchanges and ‘silencings’ across political configurations that are central to the rise of science on the global stage.”

 

Over the past two years, with funding from UK’s Arts and Humanities Research Council, he and Schaffer have undertaken a programme of debates to ask whether a transregional rather than a Eurocentric history of science could now be told.

 

To do so, they teamed up with researchers in India and Africa, including Professor Irfan Habib from Delhi’s National University of Educational Planning and Administration and Professor Dhruv Raina of Jawarhalal Nehru University, and in December 2014 held an international workshop at the Nehru Memorial Library in New Delhi. “And now our debate is also being carried forward by a new generation of early-career researchers who came to the workshop,” added Sivasundaram.

You can watch Shaffer and Sivasundaram discuss the project and some of its challenges here:

 

Source and Image: The history of science has been West-centric for too long – it’s time to think global

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No, Scientists Have Not Found the ‘Gay Gene’ – The Atlantic

This Thursday, Michael Balter at Science Magazine (and many others) reported that geneticists had found “that epigenetic effects, chemical modifications of the human genome that alter gene activity without changing the DNA sequence, may have a major influence on sexual orientation.” As Balter observes, such a finding could be welcome news for LGBTQ rights advocates, as it would combat those who argue that homosexuality is a “lifestyle choice.” On the other hand, such a finding could suggest the possibility of biomedical interventions, a prospect that I find very disturbing.

Fortunately, Ed Yong of The Atlantic dropped some common sense and statistics on the whole affair:

The problems begin with the size of the study, which is tiny. The field of epigenetics is littered with the corpses of statistically underpowered studies like these, which simply lack the numbers to produce reliable, reproducible results.

 

Unfortunately, the problems don’t end there. The team split their group into two: a “training set” whose data they used to build their algorithm, and a “testing set”, whose data they used to verify it. That’s standard and good practice—exactly what they should have done. But splitting the sample means that the study goes from underpowered to really underpowered.
If you use this strategy, chances are you will find a positive result through random chance alone.

 

There’s also another, larger issue. As far as could be judged from the unpublished results presented in the talk, the team used their training set to build several models for classifying their twins, and eventually chose the one with the greatest accuracy when applied to the testing set. That’s a problem because in research like this, there has to be a strict firewall between the training and testing sets; the team broke that firewall by essentially using the testing set to optimise their algorithms.

 

If you use this strategy, chances are you will find a positive result through random chance alone. Chances are some combination of methylation marks out of the original 6,000 will be significantly linked to sexual orientation, whether they genuinely affect sexual orientation or not. This is a well-known statistical problem that can be at least partly countered by running what’s called a correction for multiple testing. The team didn’t do that. (In an email to The Atlantic, Ngun denies that such a correction was necessary.)

So it seems that this is probably all just a case of bad scientific methodology; yet another instance of scientists abusing significance measures to manufacture spurious findings. Which should come as no surprise, given that it is absurd to think there could be such a simple genetic cause of such a complex trait as sexual orientation.

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The War on Science?!

Popular Canadian YouTube channel AsapSCIENCE has a video going around this week entitled “The War on Science”. It rightly calls out worrying trends such as the dismissal by many of the overwhelming evidence for human-caused global warming, the thoroughly debunked and yet persistent myth that vaccines cause autism, the ever-decreasing share of public funds going to scientific research, and the muzzling of public scientists. I love science, I hate all of the misinformation that is spread about climate science and medicine, and I think it is vital for our democracies for scientists to be free to speak about their research however they like.

On the other hand, as a historian and philosopher of science, I cringe at the parade of clichés and dubious claims in this video. There’s the classic “linear model” rhetoric that, although we cannot predict how, basic scientific research will lead to technical progress. There’s the indefensible value-neutrality science “simply adheres to evidence” argument. And the Roman Empire collapsed because… they didn’t pursue scientific research?

I wish HPSers could get together to make a really bang-up viral video that we could all endorse unequivocally, but perhaps it’s the nature of our discipline that this is impossible?

 

Source and Image: https://www.youtube.com/user/AsapSCIENCE

Steve Fuller’s False Hope in IDism: The Discovery Institute’s Anti-Transhumanism, Gregory Sandstrom « Social Epistemology Review and Reply Collective

SERRC: Steve Fuller’s False Hope in IDism

I know Steve Fuller mostly for his critiques of mainstream science and philosophy of science, for example in Social Epistemologyand his proposals for radically democratizing science, for example in The Governance of Science. Of course Steve is also well-known for his defense of Intelligent Design Theory as science, but I had always viewed this defense as in service of his democratization agenda, rather than as reflecting his genuine beliefs. Perhaps I should have known better given that Fuller has written multiple books on the subject. Recently, Fuller has come out as an advocate of transhumanism, a subject I know nearly nothing about.

Gregory Sandstrom’s pointed review of Fuller’s relationship to the ID movement in the context of his transhumanism was therefore very enlightening for me. Sandstrom’s central contention is that Fuller’s transhumanism is incompatible with Intelligent Design Theory, at least as practiced by the Discovery Institute (the primary institution promoting ID’s intellectual and political activities):

In his SERRC paper “Science without Expertise: Defending My Defence of Intelligent Design (Nearly) a Decade Later,” (2014) Fuller speaks of “ID and Trans-humanism.” Yet he obviously does not have the DI’s version of ID in mind when he links these two notions. Instead, Fuller has a significantly different view of ‘intelligent design’ that he is proposing, which I call cybernetic-ID (forthcoming 2015). Onlookers might wonder how or if Fuller confronts the anti-trans-humanism of the DI or if he has found some way to distinguish their IDism from his own social epistemology. This article puts Fuller’s trans-humanism and the DI’s anti-trans-humanism in sharp contrast.

 

The DI is fiercely and conservatively against trans-humanism. If Fuller wants to promote ID, trans-humanism and his so-called ‘new eugenics,’ then it would help if he distinguished his position from the politically entrenched leaders and fellows of the DI. Not to do this serves only to confuse IDists who rant against human enhancements and human-technology ‘uplift’ with Fuller’s starkly different vision for the future. This is perhaps most severely stated in what Dr. Michael Egnor says of trans-humanists displaying “shades of Mengele.” For the DI, Fuller’s trans-humanist eugenics is a dangerous threat to humankind, not just in the USA, but globally and people like Fuller are comparable to Joseph Mengele (German ‘angel of death’ doctor in Auschwitz) and therefore best removed from polite society.

I was also interested to hear Sandstrom’s account of Fuller’s religious views and how they relate to all of this:

When we read Fuller’s version of ‘trans-humanism’, we must nonetheless remember that it is at its deepest root framed within a Unitarian worldview. Since writing in 2008, “I am a secular humanist who has been steeped in the historical and philosophical relations between science and religion since my school days with the Jesuits” (2008, 8), he has more recently stated his worldview as a “non-conformist Christian” Unitarian (2014, 7). “By ‘Unitarian’ we mean the idea that each person’s connection to the original creative deity is direct and personal,” Fuller writes. “Unitarians believe that we ‘always already’ have God within us but perhaps not the means to realize our divine potential.” (2014, 5) Thus, in seeking to reach his divine potential, we see Fuller identifying his position as having closer affinities with Ray Kurzweil, Norbert Weiner and Herbert Simon (all of whom are/were more commonly considered as Jewish atheists or agnostics than mainstream Unitarians), rather than with (non-Jewish) atheist trans-humanists like Zoltan Istvan or Nick Bostrom. There are notably other non-Unitarian theists who also discuss and even promote trans-humanism, e.g. Ted Peters and Carl Teichrib that Fuller does not appear to endorse.

In reply to Sandstrom, Fuller acknowledges that his account is essentially correct, though Fuller notes that he has long been aware of the tensions between his view of ID and the Discovery Institute’s. However, Fuller believes his energies are best spent defending his transhumanist agenda from opponents on the other end of the theological spectrum:

Source and Image: Steve Fuller’s False Hope in IDism: The Discovery Institute’s Anti-Transhumanism, Gregory Sandstrom « Social Epistemology Review and Reply Collective

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Science Magazine: Climate scientist requesting federal investigation feels heat from House Republicans

In Merchants of Doubt, Naomi Oreskes and Erik M. Conway showed how attempts by the tobacco industry to avoid regulation paralleled attempts by the fossil-fuel industry to do so. The tobacco industry consciously enlisted scientists in an extended campaign to sow doubt about whether smoking caused cancer, while the fossil-fuel industry has done the same to sow doubt about global warming. Perhaps the most fascinating part of Oreskes and Conway’s story is that in many cases, these are the same scientists.

Given this context, it makes sense that some climate scientists would attempt to employ the same legal tactics against the fossil fuel industry as were successfully used against the tobacco industry. Science reports:

Senator Sheldon Whitehouse (D–RI)… noted that federal prosecutors had used the federal Racketeer Influenced and Corrupt Organizations Act (RICO)—originally developed to combat organized crime and corrupt unions—to sue the tobacco industry for covering up the health effects of smoking. And he suggested they could do the same to investigate fossil fuel firms that he charged were “funding a massive and sophisticated campaign to mislead the American people about the environmental harm caused by carbon pollution.”

 

Last month, 20 climate scientists, led by Shukla, picked up on the idea of using RICO. In a 1 September letter to President Barack Obama, Attorney General Loretta Lynch, and White House science adviser John Holdren, they wrote that “if corporations in the fossil fuel industry and their supporters are guilty of the misdeeds that have been documented in book and journal articles, it is imperative that these misdeeds be stopped as soon as possible.”

 

Other signers of the RICO letter include climate researchers from George Mason as well as the University of Washington, Seattle; Rutgers University in New Jersey; the University of Maryland, College Park; and Columbia University.

However, the political landscape in the United States these days has made this strategy difficult, and perhaps even dangerous:

Last week, Representative Lamar Smith (R–TX), the chairman of the science panel of the House of Representatives, announced plans to investigate a nonprofit research group led by climate scientist Jagadish Shukla of George Mason University in Fairfax, Virginia. He is the lead signer of a letter to White House officials that urges the use of an antiracketeering law to crack down on energy firms that have funded efforts to raise doubts about climate science.

 

In a 1 October letter, Smith asked Shukla, who is director of the independent Institute of Global Environment and Society (IGES) in Rockville, Maryland, to preserve all of the “email, electronic documents, and data” that the institute has created since 2009. Smith’s panel soon may be asking for those documents, the letter suggests.

To be clear, it appears that the chairman of the House of Representatives is proposing not to investigate possible organized attempts by massive corporations to deceive the American public about the science of climate change, but to investigate the group that wants that to happen. Democracy!

Source and image: http://news.sciencemag.org/policy/2015/10/turnabout-house-republicans-say-they-ll-investigate-climate-scientist-requesting

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Born that way? ‘Scientific’ racism is creeping back into our thinking. Here’s what to watch out for. – The Washington Post

Born that way? ‘Scientific’ racism is creeping back into our thinking. Here’s what to watch out for. – The Washington Post

Yesterday, Ellie’s Weekly Roundup referenced an editorial in the Washington Post arguing that “‘Scientific’ racism is creeping back into our thinking.” The authors see this trend in the media, in science, and in policy. Some examples:

Consider a recent paper that argues that ethnic conflict throughout history is a result of genetic diversity among communities. The authors argue that genetic diversity is the dominant force behind conflict among groups. It pushes religious communities into battle, causes distrust among neighbors and dictates support for problematic social policies. Such an argument places the history and future of human conflict in genes, as if human interaction and environmental influences cannot match their power.

For instance, in the wake of the 2012 Olympics, nearly one-third of the news articles that evoked race, genetics and athletics posited that African American and West Indian sprinters are fastest because they descend from testosterone-heavy ancestors who survived the brutal conditions of transatlantic slave trade—a belief that found resonance and widespread acceptance in a BBC-produced documentary entitled, “Survival of the Fastest.” But there is no gene or allele for “speed,” and no direct link between testosterone and speed (while sprinters may have high testosterone, not all high-testosterone people can sprint).

A highly-praised volume by journalist Nicholas Wade, “A Troublesome Inheritance,” posited that recent genetic and genomic research suggests that Africa’s underdevelopment was a result of genetic inferiority of the communities on the continent, eschewing the devastating effects of colonialism.

I’m not convinced that there is anything new in any of these examples or that we are in the midst of a “resurgence” of scientific racism, though if there is such a trend I’d look to the rise of evolutionary psychology as an obvious source. However, the potential social damage of such studies seems obvious.

Cases like these, where scientific claims can have detrimental social consequences, are a major interest of social epistemologists. Heather Douglas, for instance, argues that in cases like this the evidential threshold for making a scientific claim ought to be higher. With so much at stake, she contends, scientists really need to be sure that they’re right before they make claims like this public. Given that the reliability of many psychological studies have recently been questioned, this seems like even more reasonable advice. In Science, Truth, and Democracy, Philip Kitcher goes even further, arguing that certain lines of research ought to be (temporarily) banned because their potential consequences are too great for our (current) society to take the risk of pursuing them. This idea is anathema to scientists, but perhaps Kitcher’s extreme solution deserves consideration of scientists aren’t able to police themselves?

Source and image: Born that way? ‘Scientific’ racism is creeping back into our thinking. Here’s what to watch out for. – The Washington Post

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Will the real skeptics please step forward?

The Associated Press reported on their blog last week that they will no longer refer to those who deny the scientific consensus on climate change as “skeptics”, but will instead call them “climate change doubters” or “those who reject mainstream climate science”. Notably, they will also not use my preferred term—“deniers”—because it is seen as pejorative.

It seems like the main push for this change comes from scientists “such as those who are part of the Center for Skeptical Inquiry” who “complain that non-scientists who reject mainstream climate science have usurped the phrase skeptic.”

Fair enough, but to me both uses of “skeptic”—referring to “skeptics” like those from the Center for Skeptical Inquiry and those who deny climate change—are suspect. “Mainstream” skeptics seem to train their skepticism only at claims that occur outside of mainstream science—homeopathy, UFOlogy, and so on. Is this true skepticism or just science boosterism? I’m inclined to think the latter.

Source and image: https://blog.ap.org/announcements/an-addition-to-ap-stylebook-entry-on-global-warming