Science Literature

There is general agreement that science education has its problems, but much less agreement about what those problems are. A helpful review has appeared in Science and it deserves to be widely discussed. Everyone in the science community is aware that critiques, peer review and reasoned argument are essential to the health of our discipline. Consensus has to be earned by this process of critical examination - which does not stop when theories become widely accepted.

"Critique is not, therefore, some peripheral feature of science, but rather it is core to its practice, and without argument and evaluation, the construction of reliable knowledge would be impossible. Whether it is the theoretician who is developing new models of phenomena or the experimentalist who is proposing new ways of collecting data, all scientists must subject their ideas to the scrutiny of their peers. But what of science education?"

Children learning science: these 7-year-olds were tackling chemistry in 1948 (source here)

The problem with much science education is that often these intellectual skills are not developed in the classroom. Students are taught an authoritative body of facts and theories in a way that encourages submission rather than critical appraisal.

"Science education, in contrast, is notable for the absence of argument. Although instructors and teachers may offer many explanations, these are not arguments. To offer an explanation of a fact is to presume it is true. An argument, in contrast, is an attempt to establish truth and commonly consists of a claim that may be supported by either data, warrants (that relate the data to the claim), backings (the premises of the warrant), or qualifiers (the limits of the claim). Some or all of these elements may be the subject of rebuttals or counter-arguments. [. . .] Consequently, science can appear to its students as a monolith of facts, an authoritative discourse where the discursive exploration of ideas, their implications, and their importance is absent. Students then emerge with naive ideas or misconceptions about the nature of science itself."

This problem is so serious that it deserves to be analysed using worldview concepts. What is our understanding of science? What conceptual model leads to a "monolith of facts" and "an authoritative discourse"? It is a "consensus" perspective of science, where 'teaching the controversy' is excluded because only uncontested science is on the curriculum. However, this version of consensus science is a betrayal of basic principles and is highly vulnerable to being steered by political, ideological or business agendas. Teaching based on this consensus model may lead to students adopting "reasoning strategies with a confirmatory bias rather than using logical criteria". Students come to realise that they are rewarded for reaching the 'right' answers rather than developing transferable critical skills.

"The common explanation of the absence of argument is that it is a product of an overemphasis by teachers, curricula, and textbooks on what we know at the expense of how we know. Deep within our cultural fabric, education is still seen simplistically as a process of transmission where knowledge is presented as a set of unequivocal and uncontested facts and transferred from expert to novice. In this world-view, failure of communication is the exception and success the norm. However, in reality, education is a highly complex act where failure is the norm and success the exception."

This week has also seen a stimulating review in the US Chronicle of Higher Education of "the latest of a now common genre of science patriotism, Nonsense on Stilts: How to Tell Science From Bunk (University of Chicago Press), by Massimo Pigliucci, a philosophy professor at the City University of New York." The reviewer, who is himself a philosophy professor, writes of science warriors who have a view of science that is 'authoritative' and 'true'.

"The problem with polemicists like Pigliucci is that a chasm has opened up between two groups that might loosely be distinguished as "philosophers of science" and "science warriors." Philosophers of science, often operating under the aegis of Thomas Kuhn, recognize that science is a diverse, social enterprise that has changed over time, developed different methodologies in different subsciences, and often advanced by taking putative pseudoscience seriously, as in debunking cold fusion. The science warriors, by contrast, often write as if our science of the moment is isomorphic with knowledge of an objective world in itself - Kant be damned! - and any form of inquiry that doesn't fit the writer's criteria of proper science must be banished as "bunk." Pigliucci, typically, hasn't much sympathy for radical philosophies of science."

So, opportunities for argument and the use of critical thinking skills are urgently needed in science education. This is the take-home message of the paper in Science. For years now, scholars open to the detection of intelligent design as a product of scientific research have sought to contribute to the debate about education. 'Teaching the controversy' has been recommended as good educational practice, providing opportunity to develop arguments and to develop critical thinking skills, only to be met with hostility and rejection. There is no controversy, opponents said, evolutionary theory is robust and has achieved the status of consensus science. Evolutionists want to present their favoured ideas as "unequivocal and uncontested". The reason they get away with such shallow reasoning is that there is a wider, more general malaise within science. This is why the Chronicle review (above) is relevant: there is a vocal group of science warriors who are largely advocates of positivism, secularism and atheism that are using science to promote philosophical naturalism. This is why these issues affect us all. This is a struggle for the freedom to follow the evidence wherever it leads, and to resist those who come to us with deductive claims about the way the world is. It is also a struggle for real education instead of indoctrination by secularists.

Arguing to Learn in Science: The Role of Collaborative, Critical Discourse
Jonathan Osborne
Science, 23 April 2010: Vol. 328, pp. 463-466 | DOI: 10.1126/science.1183944

Abstract: Argument and debate are common in science, yet they are virtually absent from science education. Recent research shows, however, that opportunities for students to engage in collaborative discourse and argumentation offer a means of enhancing student conceptual understanding and students' skills and capabilities with scientific reasoning. As one of the hallmarks of the scientist is critical, rational skepticism, the lack of opportunities to develop the ability to reason and argue scientifically would appear to be a significant weakness in contemporary educational practice. In short, knowing what is wrong matters as much as knowing what is right. This paper presents a summary of the main features of this body of research and discusses its implications for the teaching and learning of science.

Science Warriors' Ego Trips
By Carlin Romano
The Chronicle Review, April 25, 2010

1st paragraph: Standing up for science excites some intellectuals the way beautiful actresses arouse Warren Beatty, or career liberals boil the blood of Glenn Beck and Rush Limbaugh. It's visceral. The thinker of this ilk looks in the mirror and sees Galileo bravely muttering "Eppure si muove!" ("And yet, it moves!") while Vatican guards drag him away. Sometimes the hero in the reflection is Voltaire sticking it to the clerics, or Darwin triumphing against both Church and Church-going wife. A brave champion of beleaguered science in the modern age of pseudoscience, this Ayn Rand protagonist sarcastically derides the benighted irrationalists and glows with a self-anointed superiority. Who wouldn't want to feel that sense of power and rightness?

Edward Wasserman and Mark Blumberg are interested in explaining the origins of novel behaviours. They are aware of several research groups working with animals and give the example of crows that were observed to fashion wires into hooks that were in turn used to gain access to food. The researchers interpreted the crow behaviour using the concepts of creativity and insight. But this is a mistake, argue Wasserman and Blumberg. The crows are learning by trial-and-error, not by forethought.

"Nonetheless, we seem to be in the midst of a resurgence of faith among some scientists that animal behavior can be explained by creativity, insight and other mentalistic concepts. For our part, we remain skeptical about the utility of such groundless explanations. Indeed, we are unconvinced that creativity and insight are proper explanations even for human behavior."

Is design a crumbling iconic concept? (source here)

The authors draw inspiration from The Evolution of Useful Things (1993) by the engineer Henry Petroski. The thesis of the book is that the design maxim "form follows function" does not reflect the history of design, and Petroski argues, instead, that "form follows failure". In other words, humans are inveterate tinkerers and indulge in experimentation; some of these avenues are found to lead somewhere and are valued, whereas others are unsuccessful and are abandoned. This leads to an incremental evolutionary process, analogous to the "survival of the fittest".

"It is through this plodding process that today's designs - typically instantiated in the form of a detailed blueprint - embody all of the hard, painful, but often unacknowledged lessons of the past. Most of us are ignorant of that history, yet we glibly proclaim that the final products were intelligently designed, thereby perpetuating the myth of the creative moment. We then carry that myth forward and attribute each new artifact to individual insight, creativity and genius."

The authors of the article are aware of the way that Darwinist thinking has impacted our culture, not just the science of origins. They suggest that even Charles Darwin and Richard Dawkins were not radical enough to apply these ideas to "that last bastion of designer intelligence, our minds". Why should our minds be exempt from being understood in Darwinian terms?

"What did Dawkins mean when he wrote of things that "really are designed"? In The Blind Watchmaker, he provided a clear answer: "All appearances to the contrary, the only watchmaker in nature is the blind forces of physics. [. . .] A true watchmaker has foresight: He designs his cogs and springs, and plans their interconnections, with a future purpose in his mind's eye" [emphasis added].
Such uncritical acceptance of purpose and foresight in human design may well be unwise. [. . .] By attributing the origins of animals and artifacts to different kinds of designers - one blind, the other intelligent - both Darwin and Dawkins lapse into the same kind of "designer thinking" that ensnared creationists like Paley."

The authors are objecting to "mentalistic explanations of behavior", and "giving human designers too much credit". In their eyes, appealing to "foresight and purpose" indicates a lack of critical thinking. The effect of all this is to bring to the fore the stimulus-response framework of behavioural psychology. This makes learning in animals and humans the result of associations being forming between stimuli and responses. The authors refer to psychologist Edward Thorndike and one of his three laws: the "law of effect" says that responses to a stimulus which are followed by a reward will be reinforced and will become habitual.

"Importantly, this positively Darwinian process exists entirely outside the realm of purpose or foresight. If everything in nature is the result of fixed laws, as Darwin himself proposed, then would he not also have marveled at the explanatory power of the law of effect - which was not discovered until several decades after his death - and its compelling parallels with natural selection?"

The authors have contributed an essay which is in the tradition of explaining human beings completely in terms of physics and chemistry. Distinctive aspects of humanity are ultimately treated as myths: consciousness, creativity, foresight and purpose. Design thinking (they suggest) should be reformulated in Darwinian terms and evolutionists should be freed from disputes over "over where to draw the line between things that really are designed and things that only appear to be designed". Some of my past blogs have considered consciousness, evolutionary psychology, Darwin's thinking about the continuity of mind, and attempts to deconstruct love. These research 'findings' have the basic premises of materialism and rationalism. Their philosophical roots are not determined scientifically (for that is impossible) but are assumed. The researchers' attempts to deconstruct humanity are destructive. Happily, they are also flawed. In the case of creativity and design, the authors point to the role of trial and error and generalize from that. What they do not do is to grapple with concepts like induction, intuition, inspiration and brain-storming. Nobody denies that a process of experimentation follows the emergence of a design concept. Most will question whether that process is best described as "trial and error" because they will expect an intelligent design of experiments rather than tinkering. The flaw is to think that because design prototypes experience (intelligent) selection, the whole process is devoid of purpose and foresight.

The main problem facing our culture is that the materialists have tried to gain a monopoly for their favoured philosophy. They are always claiming that you have to be a materialist to do science. This means that they have an easy ride in the journals and in academic forums. Roll on the day when this straightjacket is removed, and scholars can follow the evidence wherever it leads.

Designing Minds
Edward A. Wasserman and Mark S. Blumberg
American Scientist, May-June 2010, Volume 98, Number 3, Pages 183f | DOI: 10.1511/2010.84.183

First paragraph: The basic argument of intelligent design was famously set forth in the watchmaker analogy of William Paley in 1802: The complexity and functionality of a watch imply a watchmaker; analogously, the complexity and functionality of living things also imply a designer, albeit one vastly more potent than a mere watchmaker. This argument rests on a simple analogy between the design of human artifacts and the design of natural forms. For the analogy to work, we must first accept that we design our inventions with purpose and foresight. On this point, most evolutionists and creationists agree. What distinguishes these two camps is that, when accounting for the origin of living things, proponents of intelligent design summon a divine creator, whereas evolutionists credit natural selection. Thus, evolutionists share with creationists the same understanding of design; they differ only in how they invoke it.

OOL researchers need chemical building blocks with which to work, and amino acids are the most basic pre-biotic molecules. The Miller-Urey route for synthesising these molecules in the primordial Earth gained instant popularity for kicking off a self-assembly process. That mechanism has been eclipsed in recent years, not least because the necessary reducing atmosphere was perceived to be unrealistic by researchers. Consequently, interest in other ways of generating amino acids is high and there has been a steady stream of publications that address the issues. One of these mechanisms is concerned with the chemistry of comet and meteorite collisions with planet Earth.

Organic molecules are found in space, but do they have anything to do with biology? (Image credit Mario Iliev, source here)

A previous blog noted Japanese research simulating chondritic meteorite impacts, producing various organic chemicals including one amino acid (glycine). A US group led by Nir Goldman, based at the Lawrence Livermore National Laboratory, has considered cometary impacts. The initial conditions were chosen to match known compositions: a mixture of water, methanol, ammonia, carbon monoxide and carbon dioxide. The mechanism under investigation is shock compression.

"When a comet strikes a planet, a shock wave travels through it as it comes to a sudden halt. This, Goldman explains, compresses the comet, and the compression wave travels through the comet faster than the speed of sound. As a result, the molecules inside deform and bonds break."

The research makes use of validated theory and extensive simulation modeling. The findings are the result of "around one million computer hours on the powerful Atlas computer cluster at Lawrence Livermore". They chose a side-on impact because a head-on collision was considered likely to destroy rather than fabricate.

"For shock compressions lasting about 20 picoseconds at temperatures up to 4,000 K and pressures about 60 gigapascals, the researchers observed formation of chains of carbon and nitrogen atoms, some parts of which were akin to chains of amino acids. When they modeled an expansion period of 50 picoseconds, the longer chains broke up into smaller components, including a glycine-CO2 complex. The overall mixture is acidic, so the glycine-CO2 complex could react with H3O+ to produce glycine and CO2 in an exothermic reaction, Goldman said."

The implications of the research are more controversial. Do the findings help or constrain speculations about panspermia or the origin of life? The answers appear to be both yes and no.

Yes, those advocates of panspermia that point to amino acids in meteorites or comets as indicating a biotic source or as evidence of a directed or undirected colonization of the galaxy need to rethink their arguments. These organic molecules appear to be products of shock chemistry, UV radiation or some other process yet to be discovered. The mere fact of their existence does not provide any basis for inferring extraterrestrial biology. Although the enantiomeric composition of some of these molecules has been deemed to point to a biotic source, this conclusion may be wrong. Mechanisms for producing left-handed molecules in extraterrestrial environments are being examined (example here). So, this casts doubt on the recent claim of Chandra Wickramasinghe that "it seems likely that interstellar organics in large measure [. . .] derive from biology". Consequently, panspermia needs to be defended on other grounds (For example, go here).

No, speculations about the origin of life are not constrained. This is because there is an unwritten rule that all prerequisites for life count as evidence for abiogenesis. Finding a planet in the habitable zone; detecting the presence of water; recovering amino acids from space - all fuel the appetites of those who think that if life can self-assemble on Earth, it can self-assemble anywhere if conditions permit! Thus, the article from Nature News refers to crashing comets creating the "potential for life" and amino acids are described as "markers of potential life".

However, the finding of science emerging from OOL research is that an availability of traces of amino acids does not suggest that life can emerge via either Law or Chance processes. It is significant that people have become familiar with the 1953 experiments of Stanley Miller, but few ever refer to his subsequent work. He spent his career trying to achieve something more significant than amino acid residues but, although other organic compounds were obtained, he repeatedly faced dead ends. "Making the amino acids made it seem like the rest of the steps would be very easy," he said in a 1996 interview with Reuters. "It's turned out that it's more difficult than I thought it would be. It's a series of little tricks. Once you learn the trick, it's very easy. The problem is learning the trick." Miller never learned the trick.

No self-assembly pathway has ever been identified and the fate of all these molecules appears to be degradation. Few in the field have even begun to grapple with the challenge of producing biologically-meaningful information. Amino acids do not create the potential for life: only intelligence deserves to be described like this.

Production of pre-biotic molecules from extraterrestrial sources
Nir Goldman, Evan J. Reed, Laurence E. Fried, I-Feng William Kuo
ACS National Meeting, San Francisco, March 21-25, 2010, Paper 281.

Abstract: It has been proposed that impacts of extraterrestrial ices on early Earth could have been partially responsible for the creation of amino acids on the planet. We present ab initio molecular dynamics simulations of shock compressed aqueous mixtures representative of astrochemical ices found on dust grains and within other celestial bodies. We discover that high shock velocities drive the synthesis of a number of transient, exotic C-N bonded species at significantly higher pressures and temperatures than previously studied. Upon quenching to lower pressure conditions we observe a simple mechanism for the formation of the alpha amino acid glycine, an important component of protein synthesis. We find that shock compression of astrophysical ices followed by rapid expansion is a viable pathway for amino acid formation on a primitive planet, that can be verified by future experimentation.

Comet crash creates potential for life
Katharine Sanderson
Nature News, 26 March 2010 | doi:10.1038/news.2010.152

Abstract: Striking a glancing blow to a planet could create the perfect conditions in a comet's icy core to create amino acids - molecules that are vital to forming life on Earth.

See also:

Deyes, R. Improbabilists, Inevitabilists and the Astonishing Mystery of Life, ARN blog (2 July 2008)

Kemsley, J. Prebiotic Comet Collision Chemistry, Chemical & Engineering News (24 March 2010)

Tyler, D. Did meteorite impacts help to spawn life? ARN Literature blog (12 December 2008)

There has been a complexity explosion in biology - the fuse was lit in 1953 when the structure of DNA was discovered, but during the past two decades we have witnessed a dramatic expansion of data pointing to unanticipated levels of complexity. The hype surrounding the Human Genome Project suggested it would give us the blueprint of human biology and, as a consequence, would provide answers to our most probing questions.

"Mina Bissell, a cancer researcher at the Lawrence Berkeley National Laboratory in California, says that during the Human Genome Project, she was driven to despair by predictions that all the mysteries would be solved. "Famous people would get up and say, 'We will understand everything after this'," she says. "Biology is complex, and that is part of its beauty.""

Is biological complexity analogous to fractal geometry? (source here)

In the early days of the revolution, the focus was on genes. This was regarded as the key that would unlock the mysteries of the cell. Genes were the providers of biological information, and the rest of the genome (98% of it) was deemed to be Junk DNA. Since this did not code for genes, the inference was made that it should be interpreted as an evolutionary artefact, unworthy of serious study.

"Few predicted, for example, that sequencing the genome would undermine the primacy of genes by unveiling whole new classes of elements - sequences that make RNA or have a regulatory role without coding for proteins. Non-coding DNA is crucial to biology, yet knowing that it is there hasn't made it any easier to understand what it does. "We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it's not," says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK."

After the Human Genome Project came the recognition of functionality for some of the non-coding DNA. The ENCODE project (which looked in detail at a portion of the human genome) found that 74-93% of DNA was translated into RNA and performed significant roles in the cell.

"Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. "Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things - such as how a cell turns on and off - is incredibly naive," says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia."

The level of complexity rose higher and higher as it became apparent that the communication within the cell is not best modelled by signalling pathways but by networks of information flows. The discipline of systems biology was created to make sense of the complexity. The verdict appears to be one of partial success, for even the systems biology approach struggles with the levels of complexity that are found.

"In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the 'virtual human'. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model."

The author of this informative feature article on complexity is Erika Check Hayden. As more and more is known, biology does not conform to the reductionist expectation of ultimate simplicity, but instead it appears ever more complex.

"[A]s sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set - a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary."

The Mandelbrot set analogy has some value, but there is a danger to it. As Hayden points out above, the apparent intricacy is actually based on a simple equation. The complexity is in the eye of the beholder. Reductionism is entirely comfortable with the Mandelbrot set. But is biology really like this? The question deserves a much more rigorous analysis. Hayden refers to Davidson's work in developmental biology and his claim to find simplicity and order. However, reductionism is not the only paradigm that incorporates simplicity and order. The concepts of complex specified information and irreducible complexity are entirely compatible with evidences of simplicity and order, yet are not explained by the reductionist approach. The domain surveyed by Hayden is home territory for the intelligent design paradigm. ID brings a perspective on biological information that takes us in a different direction to the Mandelbrot set analogy for biological complexity. The main problem for ID has nothing to do with relevance, but with its incompatibility with a materialist approach to science. But this also is a philosophical issue deserving of the widest possible discussion within the scientific community.

Human genome at ten: Life is complicated
Erika Check Hayden
Nature, 464, 664-667 (31 March 2010) | doi:10.1038/464664a

The more biologists look, the more complexity there seems to be. Erika Check Hayden asks if there's a way to make life simpler.