How OOL science can earn some respectability.

Announcing New Sewell Prize in Biological Origins Studies!
David Klinghoffer | @d_klinghoffer

Over at Uncommon Descent, mathematician Granville Sewell announces a new prize he will be administering. It sets a fascinating challenge but offers an enviable reward:

I plan to award a prize to anyone who can invent a non-trivial 3D machine which can replicate itself. The machine must be able to make copies of itself without human intervention, except possibly to supply the raw materials. Basically a 3D printer which can print a copy of itself which retains the ability to print a copy of itself, which… A page which can be photocopied does not count, because it is the photocopier which actually makes the copy, unless the photocopy machine also makes a copy of itself; a computer program which duplicates itself does not count unless the computer it runs on makes a copy of itself also.

The reward isn’t cash but something even better: 

The prize: the right to speculate about how life originated. Leave your artificial species alone and see how many generations it lasts before going extinct. If it makes accurate copies of itself for 100+ generations, then you also get to speculate about how genetic duplication errors might accumulate into major evolutionary advances.

Now go to it, you proponents of unguided abiogenesis and evolution through all sorts of brute unintelligent, and only unintelligent, natural forces. The first ever Sewell Prize in Biological Origins Studies awaits!

Blinded by fuzzy math?

Behe on Darwinism’s “Socially Inherited Dependence on Classical Yet Irrelevant Math”
David Klinghoffer | @d_klinghoffer

“Natural selection, irreducible complexity, and random mutation all reinforce each other to make Darwinian evolution very limited,” explains biochemist Michael Behe on a new ID the Future episode. That means Behe must tackle a tough question: if the limits of Darwinian evolution are so clear, as he shows in his new book Darwin Devolves, why do gifted scientists like Richard Lenski and Joseph Thornton persist in hanging on to the failed theory, against the evidence of their own experiments? 

Talking with host Andrew McDiarmid, Behe traces the errant thinking to an outdated mathematical picture taken from Ronald Fisher (1890-1962) and his 1930 book, The Genetical Theory of Natural Selection. This highly influential work was written before scientists knew what genes actually are. It’s not surprising that Fisher missed the role of broken genes in containing the creative potential of unguided evolution.

Through “a socially inherited dependence on classical yet irrelevant math,” present-day researchers are saddled with Fisher’s own “hopeful ignorance.” Download the podcast or listen to it here.

A fatwa from one of Darwinism's ayatollah's

Do Evolutionary Principles Derive from Observation, or Are They Imposed on It?
Evolution News & Views February 25, 2016 11:25 AM

Geneticist Dan Graur of the University of Houston is implacably opposed to intelligent design -- and brutally honest about his opposition, which makes for bracing clarity in what he writes. Recently he tweeted the following 12 principles of evolution, which he drafted.

You have to love Graur's principles, because they capture orthodox neo-Darwinism in its purest form:

All of Evolutionary Biology in 12 Paragraphs, 237 Words, and 1,318 Characters

Evolutionary biology is ruled by handful of logical principles, each of which has repeatedly withstood rigorous empirical and observational testing.

The rules of evolutionary biology apply to all levels of resolution, be it DNA or morphology.

New methods merely allow more rapid collection or better analysis of data; they do not affect the evolutionary principles.

The only mandatory attribute of the evolutionary processes is a change in allele frequencies.

All novelty in evolution starts as a single mutation arising in a single individual at a single time point.

Mutations create equivalence more often than improvement, and functionlessness more often than functionality.

The fate of mutations that do not affect fitness is determined by random genetic drift; that of mutations that do affect fitness by the combination of selection and random genetic drift.

Evolution occurs at the population level; individuals do not evolve. An individual can only make an evolutionary contribution by producing offspring or dying childless.

The efficacy of selection depends on the effective population size, an historical construct that is different from the census population size, which is a snapshot of the present.

Evolution cannot create something out of nothing; there is no true novelty in evolution.

Evolution does not give rise to "intelligently designed" perfection. From an engineering point of view, most products of evolution work in a manner that is suboptimal.

Homo sapiens does not occupy a privileged position in the grand evolutionary scheme.

It's fun to play around with these. Take principle 10 seriously, for instance, and taxonomically restricted genes (so-called "orphans") represent a significant puzzle to neo-Darwinian evolution. The deepest question, of course, is this: Do these principles -- in particular, numbers 4 through 12 -- derive from observations, or are they imposed on observations?

Historical parallel:

And we recall that Galileo never made use of Kepler's ellipsi, but remained to the end a true follower of Copernicus who had said "the mind shudders" at the supposition of noncircular, nonuniform celestial motion.

(Gerald Holton, Thematic Origins of Scientific Thought, Harvard University Press, p. 64)

Indeed, one could take this catechism to London in November, to the Royal Society meeting on alternatives to neo-Darwinism, as a template for where heresy may be expected to arise.

The end of innocence?

"People Are Starting to See Scientists the Way They Really Are"

David Klinghoffer 

The public used to see politicians in far more exalted terms than they do now. The same fate befell the clergy. Now it's scientists.

Dr. Ivan Oransky, MD, of Retraction Watch gets a delicious write-up from Forbes:

Among the American public, trust in professional scientists and scientific journals is declining. Yet an overwhelming majority still believes that science "remains a source for good in the world." Could the public be on to something? Medical-doctor-turned-journalist Ivan Oransky thinks so. And it's a growing problem.

As editor and publisher of Retraction Watch, a closely followed industry blog that tracks peer-reviewed journal articles withdrawn from publication, Oransky is raising awareness of the impact that competition for grants and career advancement is having on the quality of the science being produced. Far from being above the fray and immune to corrupting influences, "Scientists are just as human as anyone else," says Oransky. And increasingly, "People are starting to see scientists the way they really are."

This is especially relevant to our concerns here:

Another major problem is that many study results cannot be reliable reproduced. Oransky cites a famous paper by Dr. John Iaonnidis, "Why most published research findings are false," that shows the inherent biases and the flawed statistical analyses built into most "hypothesis driven" research, resulting in publications that largely represent "accurate measures of the prevailing bias."

Scientific pronouncements as an "accurate measure of the prevailing bias" -- those are words to commit to memory. When we say things like that, they say we're "anti-science." No, just pro-realism about scientists.

Also quoted, Dr. Thomas Stossel of Harvard Medical School:

"I realized how fundamentally honest business people are compared to my academic colleagues, who'd run their grandmothers over for recognition."

As for non-scientists who have not yet been disabused of their childlike faith, one can only say: Growing up is hard to do.

On the echo chamber called settled science.

How Consensus Can Blind Science
Evolution News & Views 

The ruins of Mayan civilization impress anyone who visits. For Harvard astronomer Avi Loeb, they spoke to him about the philosophy of science then and now. Recounting his experience for  Nature, he describes the questions that came to his mind:

This summer, I visited the Mayan city of Chichén Itzá in the Yucatán Peninsula, Mexico. It has an ancient observatory where priest-astronomers made detailed astronomical observations around AD 600-1200. The ruins -- stepped pyramids, temples, columned arcades and other stone structures -- reveal that astronomy was at the heart of this sophisticated society.
The Mayans accurately tracked changes in the positions and relative brightness of the Sun, Moon, planets and stars. They documented their astronomical data in folding books called codices, with many more quantitative details than other civilizations at the time. The priest-astronomers used observations and advanced mathematical calculations to predict eclipses, and devised a 365-day solar calendar that was off by just one month every 100 years.

So why, I wondered, didn't the Mayans go further and infer aspects of our modern understanding of astronomy? They determined the orbital periods of Venus, Mars and Mercury around the Sun, but Earth was at the centre of their Universe.

Dr. Loeb knows he is a leading figure in today's consensus views in astronomy and cosmology. But unlike some others in his profession, he did not merely dismiss the Mayan achievements as works of a backward people lost in religious superstition. Turning his contemplations inward, he asked, "Have we learned our lesson, or is today's science similarly trapped by cultural and societal forces?"

Loeb pondered how the Mayans' detailed calculations were used to support a civilization that engaged in human sacrifice and planned warfare by the stars. "I came to appreciate how limiting prevailing world views can be," he says. In their day, Mayan astronomers were held in high social esteem. So are today's astronomers. Loeb thought about how "Cosmologists today collect vast amounts of exquisite data in surveys of large parts of the sky, costing billions of dollars." But Good data are not enough, he realized.

What might have helped the Mayans break out of the box of their prevailing world view? He hit upon a solution that should be of great interest to the intelligent design community.

The consequences of a closed scientific culture are wasted resources and misguided 'progress' -- witness the dead end that was Soviet evolutionary biology. To truly move forward, free thought must be encouraged outside the mainstream. Multiple interpretations of existing data and alternative motivations for collecting new data must be supported.
We hasten to clarify that so far as we know, Dr. Loeb is not an advocate of intelligent design, even though he has proposed a design inference for SETI . His advice, though, harks back to Darwin's own admonition: "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question." The question in Darwin's day was design v. naturalism, as it is today. When it comes to origins, there aren't any other options. Either the universe is designed, or it is not. Would it not be limiting to the prevailing world view to assert that naturalism is the only side of the question?

Loeb gives a brief catalog of massive projects being funded by NASA and ESA. But then he gives a Kuhnian view of these efforts. Today's astronomers and cosmologists work within a paradigm as members of a guild who cannot see outside their project. Anomalies do not alarm them, as they should. Instead, they focus their attention of puzzle-solving to establish the paradigm -- not to overthrow it.

Such projects have a narrow aim -- pinning down the parameters of one theoretical model. The model comprises an expanding Universe composed of dark matter, dark energy and normal matter (from which stars, planets and people are made), with initial conditions dictated by an early phase of rapid expansion called cosmic inflation. The data are reduced to a few numbers. Surprises in the rest are tossed away.
I noticed this bias recently while assessing a PhD thesis. The student was asked to test whether a data set from a large cosmological survey was in line with the standard cosmological model. But when a discrepancy was found, the student's goal shifted to explaining why the data set was incomplete. In such a culture, the current model can never be ruled out, even though everyone knows that its major constituents (dark matter, dark energy and inflation) are not understood at a fundamental level.

He's absolutely right; in recent news reports, dark matter remains as mysterious as ever. Astronomers have leapfrogged from WIMPs to MACHOs to axions, finding no evidence for any of them, despite expensive searches with super-sensitive detectors. Perhaps a candidate particle will turn up some day, but without empirical evidence, have physicists improved on Mayan divination? Dark energy is even more mysterious. Nobody has any idea what that is. And there's more darkness:

How each culture views the Universe is guided by its beliefs in, for example, mathematical beauty or the structure of reality. If these ideas are deeply rooted, people tend to interpret all data as supportive of them -- adding parameters or performing mathematical gymnastics to force the fit. Recall how the belief that the Sun moves around Earth led to the mathematically beautiful (and incorrect) theory of epicycles advocated by the ancient Greek philosopher Ptolemy.
Similarly, modern cosmology is augmented by unsubstantiated, mathematically sophisticated ideas -- of the multiverse, anthropic reasoning and string theory. The multiverse idea postulates the existence of numerous other regions of space-time, to which we have no access and in which the cosmological parameters have different values.

We can become "blinded by beauty" that keeps us attracted to our own beliefs. Loeb mentions some paradoxes in cosmology that hint the consensus is on the wrong track. Modern cosmology is not knowledge, he says; it is organized ignorance! Only openness to other approaches can help reveal the extent of it.

Cultivating other approaches avoids stalling progress by investing only in chasing what might turn out to be 'epicycles'. After all, the standard model of cosmology is merely a precise account of our ignorance: we do not understand the nature of inflation, dark matter or dark energy. The model has difficulties accounting for the luminous gas and stars that we can see in galaxies, while leaving invisible what we can easily calculate (dark matter and dark energy). This state of affairs is clearly unsatisfactory.
The only way to work out whether we are on the wrong path is to encourage competing interpretations of the known data.

ID proponents might take advantage of Loeb's appeal in a way Paul Nelson relates in the new film Origin:

Often, when I'm reading the origin-of-life literature, considering some proposal for the formation, let's say, of RNA or proteins -- and even the author admits it's chemically implausible -- and I ask myself, How did he get himself into this jam?...
And at that impasse I want to say to the author, Look you know it's implausible, I know it's implausible, the reason that you ended up here standing at the edge of this cliff staring at implausibility is because way back down the road you decided that only a materialist explanation would work.

Dr. Timothy Standish adds:

How many different explanations that fail within the materialistic box do we have to have before we decide, maybe we need to move outside of that box. Maybe we need another kind of explanation.
When it comes to cosmology, Dr. Loeb is painfully aware of implausibilities in the naturalistic box: dark matter, dark energy, inflation, the multiverse, and the Anthropic Principle. But he is not just standing at the cliff, staring at implausibility; he is welcoming new thinking outside the box. It's an opportunity for a meaningful discussion of alternatives. And it was published in Nature, the world's leading science journal.

A healthy dialogue between different points of view should be fostered through multidisciplinary conferences that discuss conceptual issues, not just experimental results and phenomenology. A diversity of views fosters healthy progress and prevents stagnation. In September, I had the privilege of founding an interdisciplinary centre, the Black Hole Initiative at Harvard University in Cambridge, Massachusetts, which brings together astronomers, physicists, mathematicians and philosophers. Our experience is that a mix of scholars with different vocabularies and comfort zones can cultivate innovation and research outside the box. Already the centre has prompted exciting insights on the reality of naked singularities in space-time, the prospects for imaging black-hole silhouettes and the information paradox.
The "information paradox" refers to the conservation of information in the case of black holes. Think about what ID has to offer the admittedly stagnant field of consensus cosmology:

Theory of information: its source and conservation

A cause to explain the fine-tuning of the universe (e.g., see New Scientist) without the "cop-out" of the Anthropic Principle (New Scientist)

Mathematics, as seen in Origin's probability calculations for the origin of life, the Universal Probability Bound, and the "No Free Lunch" theorems

Philosophy of science unlimited by naturalism

A different vocabulary and comfort zone

Research outside the box

Loeb concludes, "Such simple, off-the-shelf remedies [i.e., multidisciplinary conferences] could help us to avoid the scientific fate of the otherwise admirable Mayan civilization." Would he extend his hand far enough to consider design? Perhaps not. But while the rise and fall of Mayan civilization is on his mind, leading him to ponder modern cosmology's potential for worldview blindness, the time seems right to engage the discussion.