Chinks in the Scientific Method

first_imgV & V. That’s shorthand in project design for “validation and verification.” Does the scientific method provide V & V? We are all taught to think that peer review, publication and replication help science to be self-checking, so as to avoid error. Some recent articles show that ain’t necessarily so. It may sound good in theory, but in practice, the ideal doesn’t always match the real.Publish and perish: In Nature (480, 22 December 2011, pp. 449-450, doi:10.1038/480449a) Adam Marcus and Ivan Oransky reminded readers of the world’s premiere science journal that in science publishing, “The paper is not sacred.” Peer review needs to continue long after a paper appears in print, they argued. Their concern was prompted by a 15-fold increase in the number of retractions over the last decade. During the same time period, papers increased by 50%. This is not necessarily bad, Marcus and Oransky continue, because it indicates corrections are being made. But what about bad papers that don’t get retracted? They pointed out disturbing cases where peer review was poorly checked by journal editors, sometimes with “massive” numbers of errors in a paper, under the excuse that peer review is supposed to be secretive. Often readers are given no explanation for a retraction other than, “This paper has been withdrawn by the authors.” Notice how extensive the problem is in their words:Editors have many reasons to pay more attention to retraction and correction notices. For one, scientists often cite papers after they’ve been retracted, and a clear, unambiguous note explaining why the findings are no longer valid might help to reduce that. But, more importantly, a vaguely worded note that includes further claims from researchers whose work has been seriously questioned, in turn raises questions about the integrity of the journal itself, and about the overall scientific record.Marcus and Oransky pointed to new online methods that might reduce the number of mistakes making their way into the corpus of “scientific knowledge”—even the radical idea that the new methods may reduce the publication of scientific papers in journals. But their article raises other serious questions. Since World War II we have been led to believe that peer review provided the V & V science needed. How do we know that new, untested methods will do better? To what extent are mistakes entering the corpus because of peer pressure instead of peer review – the demands of universities to measure a scientist’s performance by how much he or she publishes? How can scientists keep up with the growing volume of publications? They raised additional questions:There are other hurdles. How should scientists treat papers that are hardly read, so are never evaluated post-publication? Does a lack of comment mean that the findings and conclusions are extremely robust, or that no one has cared enough to check? Including readership metrics alongside comments should help here.The authors could only hope that additional scrutiny and new methods will “make the scientific record more self-correcting.” That implies that the self-correcting nature of science we have been trusting is not doing a very good job.Replicate and perish: In theory, scientific errors are caught because other scientists try to replicate the experiment. This may have worked for high-profile claims like cold fusion, but how would someone replicate a discovery of the Higgs boson without a second Large Hadron Collider? Earlier this month, Science Magazine printed a special series on replication. In the introductory article, “Again and Again, and Again,” (Science, 2 December 2011: Vol. 334 no. 6060 p. 1225, doi: 10.1126/science.334.6060.1225 ), Jasny, Chin, Chong and Vignieri began, “Replication—The confirmation of results and conclusions from one study obtained independently in another—is considered the scientific gold standard.” That’s the theory. In practice, they found enough dross in the crucible to be worried: “New tools and technologies, massive amounts of data, long-term studies, interdisciplinary approaches, and the complexity of the questions being asked are complicating replication efforts, as are increased pressures on scientists to advance their research.” The series of articles that followed showed why replication is often unreachable in the real world. How do you get a rare animal, say an ivory-billed woodpecker (or a Loch Ness monster, for that matter), to appear on cue, so that an observation can be replicated? Unique experiences in the field challenge the gold standard: “although laboratory research allows for the specification of experimental conditions, the conclusions may not apply to the real world,” they said. Consider, also, the difficulty of replicating medical tests, which might involve thousands of patients in longitudinal studies lasting years. Other questions the authors did not mention could be asked. To what extent does a shared paradigm, or shared beliefs, decrease the motivation to attempt replicating a popular result? Remember the recent decade-long fraud by superstar Diederich Stapel (11/16/2001, 11/05/2011). More significantly, if science cannot live up to its own ideals of peer review and replication, what right does it have to claim epistemic superiority over other departments in the academy?Reduce and perish: How big does a sample have to be to arrive at a sound conclusion? That’s what Medical Xpress asked in an article, “The perils of bite-size science.” Two psychologists are worried about a trend toward shorter papers and smaller samples (a principle applicable to any scientific field, not just psychology). Yes, people may enjoy reading shorter papers—but now there are more of them, and publishers have to do more work, contrary to their hope that word limits would simplify things. Worse, since small sample sizes can lead to false positives and wrong conclusions, “two short papers do not equal twice the scientific value of a longer one,” the researchers argued. “Indeed, they might add up to less.”Yet the psychologists’ implicit contention that longer, more detailed papers are more reliable may not be true. In fact, they pointed to other factors that can undermine the credibility of any paper, short or long. Consider these three steps to misinformation: (1) “surprising, ‘novel’ results are exactly what editors find exciting and newsworthy and what even the best journals seek to publish”; (2) “The mainstream media pick up the ‘hot’ stories”; (3) “And the wrong results proliferate.” The trend toward bite-size science is leading scientists away from the healthy skepticism on which science depends, the authors believe.Form a consensus and perish: Scientists like to be objective, not subjective. But Andrew Curtis (U. of Edinburgh) argues that science cannot rid itself of subjectivity. In his essay “The Science of Subjectivity” published in the journal Geology (open access, Geology v. 40 no. 1 p. 95-96, doi: 10.1130/focus012012.1), he reminded geologists that subjectivity is built into the scientific method:While the evidence-based approach of science is lauded for introducing objectivity to processes of investigation, the role of subjectivity in science is less often highlighted in scientific literature. Nevertheless, the scientific method comprises at least two components: forming hypotheses, and collecting data to substantiate or refute each hypothesis (Descartes’ 1637 discourse [Olscamp, 1965]). A hypothesis is a conjecture of a new theory that derives from, but by definition is unproven by, known laws, rules, or existing observations. Hypotheses are always made by one individual or by a limited group of scientists, and are therefore subjective—based on the prior experience and processes of reason employed by those individuals, rather than solely on objective external process. Such subjectivity and concomitant uncertainty lead to competing theories that are subsequently pared down as some are proved to be incompatible with new observations.Curtis presented a fairly positivist view that science will guide itself from the subjective to the objective. Subjectivity can even be good for science. “Allowing subjectivity is a positive aspect of the scientific method: it allows for leaps of faith which occasionally lead to spell-binding proposals that prove to be valid,” for instance. (He did not provide statistics of valid vs. nutty spell-binding proposals). But he cautioned readers to realize that even quasi-objective methods, like the popular Bayesian analysis, have built-in subjective aspects.A study of how geologists arrived at a consensus pointed to the influence of group dynamics. One study showed that geologists were influenced to change their previously-solid opinions as a result of interacting with colleagues. A particular geologist changed his mind twice because of what the group did. Curtis pointed to several studies that illustrated similar kinds of group dynamics at work. What is the upshot?The above studies significantly influence the way one should interpret consensus-driven results. Consensus positions clearly may only represent the group opinion at one instant in time, and may not represent the true range of uncertainty about the issue at hand (e.g., Fig. 1C). This is disturbing because consensus is often used in the geosciences.As an example, he pointed to climate change: “IPCC conclusions are all consensus driven—positions agreed between groups of scientists.” While consensus formation may soften the bias of the overconfident, “the group consensus approach may also introduce dynamic biases … which are more difficult to detect without tracking the dynamics of opinion. ” What this means is that the herd mentality operates even in scientific meetings. It takes courage to be a lone ranger, but the maverick might be right.Better late than never? Sigmund Freud is a fallen superstar, once exalted within the triumvirate of modern movers along with Marx and Darwin. He has even been compared to Copernicus. His theory of psychoanalysis spawned a whole industry of couch-side therapists, using Freud’s new vocabulary that lent scientific credibility to his ideas. Guess what: psychoanalysis never existed. That’s what New Scientist reported, based on new revelations that have come to light in The Freud Files:The Freud Archives, a collection of letters and papers, were deposited at the US Library of Congress by Freud’s daughter, Anna, to put them out of reach of unofficial biographers. This move also locked away Freud’s patients’ versions of their own problems.But now, as primary material is made public, parts of the archive are declassified and his letters re-edited without censorship, the legend is “fraying from all sides”.Freud was a legend in his time, and apparently a legend in his own mind. This should sound alarm bells. How could a large portion of academia be duped for so long? What legends are we following today that will be exposed as tomorrow’s frauds?Science for dummies: In a strange paper that sounds like a script for Revenge of the Nincompoops, Peter Fiske invited the scientific community to “Unleash Your Inner Dummy.” That’s right; in Nature itself (Nature 480, 7 December 2011, p. 281, doi:10.1038/nj7376-281a), he argued that “There is something to be said for letting go of the mantle of expert.” Intelligence, intellect, and prestige are valued in academia, but nincompoops have all the fun:Ironically, always playing the expert can be limiting, in terms of both contributions to science and career options. Sometimes, playing the dummy can be liberating and help to reveal opportunities that would otherwise have been overlooked. Dummies ask questions that experts assume were answered long ago. Dummies explore subject areas in which they lack knowledge. Dummies listen more and talk less.The mantle of expertise, in other words, can be a choke rag. Loosen up, he says, and ask the dumb questions. It’s OK to kick a sleeping dogma:Becoming a dummy frees you from dogma. Developing expertise can often mean ingesting unquestioned assumptions and accepted facts. Such received beliefs can lead to unchallenged group decision-making and prevent a community from recognizing a path-breaking discovery — especially when it comes from someone outside the discipline.What a radical concept. Could it be that the next great idea will come from a dummy, someone not tied to the paradigm? It’s happened. Moreover, Fiske argues, “Embracing your inner dummy is also a powerful tool for communicating science.” Scientists in the role of expert talk down to the public and think all they need is facts, when maybe it would be good for them to humble themselves and “seek to understand the audience’s cultural and ethical perspectives.” Let’s hear it for thinking outside the box.This journey into the engine room of science has been brought to you by the dummies at Creation-Evolution Headlines, who are too stupid to realize that evolution is a fact, because the scientific consensus says so. But oh, do we have more fun. Come out, come out, ye Darwin Dogmatists, and see the beauty of the cultural and ethical perspectives. Loosen your tie that binds you to the consensus. Ask the dumb questions. Do some peer review on peer review. Check to see if peer pressure is undermining the pier on which the amusement park of science sits. Exercise your autonomy: doubt a publication, question a Project Scientist, vote against the crowd. Trust not in a flawed human enterprise. Freud has fallen. Marx has fallen. Darwin is next. Turn in your false gods for a true One. Recognize that while logical thinking, clarity and accuracy are noble traits, they are not the exclusive property of scientists – a word invented in 1832 by William Whewell for natural philosophers, ostensibly to energize their group dynamics, but has resulted in an elitist class of self-proclaimed experts who know more and more about less and less until they know absolutely everything about nothing that really matters. You matter more than matter. It’s all about soul – the soul of science, which is faith in a unified, sensible, created order that points to its Source. Become a dummy in the world’s eyes, that you may begin to become truly wise (I Corinthians 2). (Visited 26 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

Paley’s Watch Found

first_img(Visited 679 times, 1 visits today)FacebookTwitterPinterestSave分享0 There actually is a clock in the heath, and it’s in our bodies, too.What is a watch? It’s an instance of a clock. William Paley famously presented his famous “watchmaker argument” in Natural Theology in 1802, a book that influenced Darwin. Paley asked what one could deduce if he ran across a watch lying upon the ground in a heath. With cogent analysis, he anticipated the arguments of Michael Behe (Darwin’s Black Box) about irreducible complexity and arguments about functional wholes of Douglas Axe (Undeniable). Whether or not Paley took his argument too far, his “watchmaker argument” can stand on its own as a logical argument for intelligent design.Since a watch is a clock, but not all clocks are watches, we need to be sure that other instances of clocks support Paley’s argument. One might dispute Paley by saying the daily rotation of the earth is a ‘clock’ of sorts that is not irreducibly complex. The point of the argument is that a designed clock has a point. It’s organized in a way to tell time for a purpose. The earth’s diurnal cycle is oblivious to beings that might use it to tell time, but a watch was made for the purpose of monitoring the passage of time for human use. The Greeks had a water clock. Early medieval people had the hourglass. Christian Huygens invented the pendulum clock. As science progressed, clocks utilizing springs and gears, then quartz vibrations, and then atomic frequencies refined timekeeping to astonishing levels of accuracy. Timekeeping devices are so accurate now that scientists routinely have to consider adding a “leap second” every few years to keep instruments in sync with astronomical phenomena, and GPS satellites have to take very tiny relativistic effects into account.Critics of Paley might say that the early timekeeping devices, like the hourglass, are not irreducibly complex (IC), because any similar repetitive process in nature could be used by a person to infer time, even if it doesn’t happen for the purpose of providing timekeeping information to humans. Examples might be tides, the rising and falling of the Nile, or a regular geyser’s eruption. At some point, human clock devices certainly became IC, because nobody would assume nature could produce a modern atomic clock.One telltale sign of an IC clock mechanism would be if it contained switches that perform a function. Most of us have seen the mechanical trippers on certain clocks that flip lights on and off. Alarm clocks that turn on a buzzer or radio station are more examples. These days, the clocks in our smartphones can switch on all kinds of applications, and the “internet of things” is beginning to link whatever function one might desire to the passage of time, so that you can even reset your home lights in New York remotely from a Paris cafe. Hourglasses lacked these additional functions. Whenever we see a clock that can switch on another function that is independently useful, we’re getting close to IC. If it can switch on numerous functions, and simultaneously respond to external inputs to keep those functions regulated within tight constraints, then the case for IC becomes very convincing. If Paley’s 1805-era watch was IC, how much more would such a time-based, adapting, switching master regulator be?The Circadian ClockNow we are ready to announce the existence of such a clock: the circadian clock in all living things. Science Magazine published a collection of papers on biological clocks recently. In a leading Perspective article, Millius and Ueda discussed why organisms need circadian mechanisms, and how new knowledge is being gained about them:An internal biological rhythm, the circadian clock—which can be measured by changes in rhythmic gene expression, cellular activity, or physiological behavior—enables an organism to anticipate daily cyclic changes in the environment.Credit: Illustra MediaWe see in this quote that the clock mechanism comes from genes, which are sequences of information – not mere rhythms of natural objects subject to laws of nature (like the tides). We see also that these genes switch on functions such as cellular activity or behavior that are important for the organism. The genes can adjust to external inputs, such as sunlight, as when we adjust to jet lag. The functions that the circadian clock switch on are numerous, the article goes on to say. Effects occur at all scales, too, from the individual protein and organ to the whole organism. Even more interesting is the finding that timekeeping functions differ between tissues. This suggests that the regulation of circadian rhythms are customized for each tissue, for each organ, and for the whole organism (e.g., for diurnal and nocturnal animals). Here’s a sample of the complexity researchers found when they measured gene expression in the tissues of one species of primate, the olive wild baboon:Approximately 11,000 transcripts were expressed in all 64 sampled tissues, which the researchers called ubiquitously expressed genes, including many involved in basic cellular functions such as DNA repair, transcription, and protein homeostasis. Most of these ubiquitously expressed genes were rhythmic in at least one tissue, but there was little overlap in rhythmic genes between tissues, which suggests that tissue-specific mechanisms control oscillatory expression. For example, a gene that had rhythmic expression in the liver was constitutively expressed in the heart. Because ubiquitously expressed genes control fundamental biological processes, timing their expression can affect the overall function of a tissue. For example, diurnal regulation of exocytosis in the thyroid or adrenal glands may enable rhythmic release of endocrine factors, compared with other organs in which the timing of exocytosis is less important for function.The Whole-Genome ClockCredit: Illustra MediaIn another Perspective article by Carolina Diettrich Mallet de Lima and Anita Göndör in Science, we learn that the whole genome itself is organized to facilitate circadian homeostasis, that is, the maintenance of accurate timekeeping in spite of external perturbations.Maps of physical contact probabilities between distant regions have earlier revealed that the genome is organized into topologically associating domains (TADs) displaying high local, intradomain chromatin-fiber contact frequencies. Given that TADs constrain and thereby increase the specificity of enhancer-promoter (E-P) contacts, the mechanisms and dynamics of TAD formation are intensely investigated.This organization that regulates gene expression is highly specific, as would be expected for homeostasis. But it also exhibits flexibility. The Perspective article references a paper in Science by Kim et al. that shows that the circadian clock is not only reliable, it is able to adapt to changing conditions.Phenotypic plasticity, the potential for phenotypic change in response to external signals, drives adaptation to environmental fluctuations and requires flexible gene regulation. A seminal example of adaptive plasticity is represented by the circadian clock, which establishes 24-hour rhythmicity in physiology, metabolic activities, and behavior. As external time cues, such as light and food intake, can reset the phase of oscillations, circadian homeostasis enables light-sensitive organisms to both anticipate and adapt to daily environmental cycles. On page 1274 of this issue, Kim et al. provide a glimpse into the genome-wide complexity of transcriptional plasticity during the physiological circadian cycle in mice, with implications for our understanding of diseases linked with deregulation of the circadian clock.The Cell Cycle ClockAnother type of clock does not need to know the time of day so much as it needs to ensure processes occur in the proper sequence. Business project managers are familiar with Gantt charts or Pert charts that lay out the sequence of steps in a project, such as what steps need to complete before other steps can begin. A foreman on the project might establish checkpoints for go or no-go decisions based on upstream events. That’s what the cell does when its project is duplicating itself. Phys.org tells how proteins regulate the cell cycle:Credit: Illustra MediaCell division is the basis of all life. Even the smallest errors in this complex process can lead to grave diseases like cancer. Certain proteins have to be switched on or off at specific times for proper cell division. Biophysicists and medical biochemists at Martin Luther University Halle-Wittenberg (MLU) have described the underlying mechanism of this process. They report how different signaling pathways in the cell change the structures of proteins, thereby driving the cell division cycle in the right direction at the right time. The researchers present their findings in Proceedings of the National Academy of Sciences.Lest anyone doubt that the cell cycle is irreducibly complex, read on:The cell cycle is an extremely complex and precisely defined process. “The parent cell has to double its existing components and then divide into daughter cells. In order to do this, numerous genes have to be switched on and off at very specific times,” says biophysicist Professor Jochen Balbach from MLU. The cell cycle is sub-divided into phases. These are controlled by what are known as inhibitor proteins, also called CDK inhibitors. Like a red traffic light, these proteins block transition to the next phase until the cell gives the relevant start signal. ConclusionPaley’s watch has been found. It was inside him all the time, as well as inside the heather on the heath. The exciting thing is, it is far more complex than Paley could have imagined. If a relatively simple watch on the ground was sufficient to infer intelligent design, how much more the regulated, flexible, switching circadian clocks described above?Exercise: Darwinians will undoubtedly rush to argue that there is an evolutionary path to the human circadian clock with all its complexity. Some early microbe found it beneficial to regulate its activity by the diurnal cycle. Later organisms got better at it, and over millions of years, here we are. How would you respond to this claim? (comments are invited). We have more to say about natural selection in a future post, but start with our March 13 entry, ‘Natural Selection? No – Sheer Dumb Luck.” The evolutionary comeback hinges on what ‘fitness’ means, and whether natural selection is a creative process with functional innovation as an expected outcome. It’s not enough to imagine a path and tell just-so stories about it. The actual random mutations that were selected need to be specified.Extra Credit: Many skeptics feel that David Hume answered Paley’s argument from design and basically overturned the case of the natural theologians. Hume, however, wrote his Dialogues Concerning Natural Religion in 1779, a full 23 years before Paley’s book came out. Imagine a debate between Hume and Paley. Who do you think would have succeeded in 1802? Who do you think would win in 2018, now that we know much more about life, genetics and the living cell?last_img read more