On origins and the design debate.

Pre darwinian design v. materialistic OOL.

In BIO-Complexity, Meyer and Nelson Debunk DRT
Ann Gauger 

Origin-of-life research has a big problem, and the DRT model purports to solve part of it. In a peer-reviewed paper published this week in BIO-Complexity,  Stephen C. Meyer and Paul Nelson take on DRT. What is DRT, exactly, you ask? Some background will help in explaining.

While DNA carries information necessary to build cells, it performs no chemistry and builds no cellular structures by itself. Rather, the information in DNA must be translated into proteins, which then can carry out the various chemical and structural functions of life. But there is no direct way to convert a given DNA sequence into a protein sequence -- no direct chemical association between DNA nucleotides and amino acids. Some sort of decoding mechanism is needed to translate the information encoded in DNA into protein.

That decoding mechanism involves a whole host of enzymes, RNAs and regulatory molecules, all functioning as an elegant, efficient, accurate and complicated system for copying and translating the information in DNA into a usable form. (For a comprehensive and engaging description of how information is processed in the cell, and how the details of this process have been discovered, see Stephen C. Meyer's  Signature in the Cell.)

The problem is, this decoding system is self-referential and causally circular. Explaining its origin becomes a chicken and egg problem. As it stands now, you need the machinery that translates DNA into protein in order to make the very same machinery that translates DNA into protein. This should give us pause, because causal circularity cannot be explained in purely naturalistic terms. In order to avoid this trap, neo-Darwinian evolution would require the prior existence of another way to specify and carry out protein-like functions in a heritable fashion, but apart from the usual machinery -- DNA, RNA and protein, all three working together.

So when it was discovered that some RNAs could carry out (very limited!) chemical reactions, scientists seeking a purely materialistic explanation for life's origin were thrilled. Perhaps here was the solution to the conundrum. Perhaps RNAs could be both catalysts and heritable information carriers. Perhaps the first living world was RNA-based.

Fast forward to now. Researchers continue to try to design RNAs that can copy themselves, and try to expand the range of chemistries they can carry out. The RNA world, if it ever existed, though, would be a very impoverished place, based on what human designers have been able to produce so far. And the problem of how an RNA world could become a DNA/RNA/protein world would still remain.

Enter the  Direct RNA Templating (DRT) model of Michael Yarus et al. His hypothesis was originally based on the discovery that the activity of one RNA catalyst could be blocked by the presence of the amino acid arginine. From this result Yarus hypothesized that perhaps other RNAs would show an affinity for particular amino acids. In a series of papers he and his coworkers identified other such RNAs. Then, based on statistical analysis,  they argued that these RNAs contained a higher than expected frequency of triplets corresponding to the particular codons or anticodons now used in the modern genetic code to specify the particular amino acid they bound.

But is their analysis correct? Meyer and Nelson carefully examine the claims of Yarus et al. and find them wanting. Inadequate null hypotheses, arbitrary selection of data for analysis, and unrealistic assumptions about prebiotic chemistry are just a few of the problems. Rather than go through their arguments here, I encourage you to read their paper yourself.

Why does it matter? Critics of intelligent design have advanced the DRT model as the answer to the sequencing problem -- how genetic information in RNA (in the hypothetical RNA world) eventually could have been translated into more stable and versatile proteins. Based on the analysis in this paper, however, the sequencing problem has not been solved, even partially. There is no natural affinity between RNAs, amino acids, and codes. And the origin of life remains inexplicable in materialistic terms.

On decanonising scientism.

Lessons from the Wansink Science Scandal

Sarah Chaffee

What pedagogical methods best prepare students to engage with science? Quality science education, especially regarding evolutionary theory, is inquiry-based, not dogmatic. 

Over at the Washington Post, Alan Levinovitz, associate professor of religious studies at James Madison University,  wrote an article reflecting on the recent Brian Wansink science scandal. He comes to the conclusion that science education often errs by omitting instruction about critical thinking. 

Who is Brian Wansink? From the Associated Press:

A prominent Cornell University food researcher resigned after an investigation found he committed academic misconduct, including misreporting data, the school announced Thursday.

Brian Wansink has been removed from all teaching and research positions and will retire at the end of the school year next June, Cornell said in a statement.

Wansink had previously helped update the U.S. dietary guidelines and is known for his research on consumer behavior, which has been widely cited including in articles by The Associated Press.

Cornell says Wansink’s academic misconduct also included “problematic statistical techniques, failure to properly document and preserve research results, and inappropriate authorship.”

Thursday’s announcement comes a day after six more of Wansink’s papers were retracted. The most recent retractions included a 2005 paper that said people eat more when served in large bowls and a 2013 article that said grocery shoppers buy food with more calories when they’re hungry.

Levinovitz describes Wansink’s fall as “painful to watch.” He had written on the professor’s studies in the past, but notes that he no longer trusts any of Wansink’s research: 

Most important, I no longer trust myself. I take pride in being a steely-eyed skeptic, wary of too-good-to-be truths. Yet my critical apparatus was hijacked by Wansink’s apparent altruism and his alignment with my own beliefs about the power of branding…

The State of Science

What does the Wansink ordeal reveal about the state of science? 

“In theory, the scientific method is objective. But in reality, science is produced, interpreted and reported by humans — humans who are fallible, biased and self-interested,” Levinovitz states. 

In the wake of the Wansink scandal, there have been renewed calls for reforming the methods and culture of scientific inquiry: open data to allow for outside verification of results, pretrial registration so researchers can’t sift through results to come up with post hoc conclusions. The intense pressure of academia’s “publish or perish” mantra is no longer seen as an engine of discovery, but rather a possible enemy of honest inquiry.

I agree. Science ought to be subject to more scrutiny. I would also add that biases in science lead to some evidence — such as evidence contrary to evolutionary theory — being excluded from mainstream publications.

“A Big Book of Important Truths”

Professor Levinovitz also wants to reform science education. “When I was a child, scientific knowledge was presented to me as though it came from a big book of Important Truths,” he notes. An approach like that does not prepare citizens to critically evaluate research like Wansink’s. 

“Reforms to the culture of science need to be accompanied by reforms in science education,” says Levinovitz. 

Textbooks should include case studies of how industry funding can skew results. The standard suite of experiments should include at least a few meant to illustrate confirmation bias. Statistical tricks such as post hoc generation of conclusions from a large data set are not difficult to understand, and they should be laid out clearly as cautionary tales.

It is important not only for critical inquiry to be used in evolutionary biology, but also for students to learn about Darwin’s theory and the modern evolutionary synthesis by practicing what it means to weigh the evidence objectively.  Our Science Education Policy calls for teaching the scientific strengths and weaknesses of evolution, noting: “[E]volution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can’t be questioned.” Why? Good science avoids dogmatism. 

Beyond Science

This is also worth pointing out: Levinovitz at the end of his article finds himself looking beyond science to the realm of ethics. “STEM education needs to emphasize moral virtues for what they really are: key features of the scientific method,” he writes. 

Wow. 

He concludes this way: 

[R]eflecting on Wansink’s fall, we should remember that what we want to believe — what’s easiest to believe — isn’t necessarily true. Insisting on believing it anyway? That’s the opposite of good science, and good scientists and science educators should lead the fight against it.

Well said. it would be interesting to know whether Professor Levinovitz sees the importance of extending this philosophy to the study of evolution.