MindBlog's half-sour pickle recipe

This posting falls under the "random curious stuff" category mentioned in the title box of this blog. At the social/musical at my Twin Valley home on June 29, several people asked for the recipe for the half-sour pickles we had served with gazpacho as a garnish. Here it is, the result of several trials to get them the way I like them. Not guaranteed to please all....

Deric's final half sour pickle recipe:

-2 lbs pickling cucumbers
-1 bundle of dill heads and stalks
-Wash cukes and dill, cut dill stalks to ~2-3 inch lengths, cut ends off cukes, slice cukes lengthwise if they are large.
-layer dill and cukes in container (~2 quart jar or plastic container)
-pour in water to cover, then pour this water into quart (4 cup) measuring cup to determine its volume, i.e. the desired volume for the pickling mixture to be added (should be ~ 4 cups).
-add 1/4 cup sea or kosher or pickling salt to 2 cups water, dissolve
-add 1/3 cup rice wine vinegar (or other very mild vinegar), 1/2 teaspoon whole black peppercorns, 3-4 whole coriander seeds, 1/2 teaspoon mustard seeds, 4-6 cloves fresh garlic, finely chopped.
-add water to obtain the volume determined above (~4 cups) while mixing thoroughly and pour over pickles.
-rotate jar or container at intervals to mix thoroughly, leave two days at room temperature, until a few bubbles start to appear, then put in refrigerator.
-pickles should be ready to eat after ~ 4 days, flavor improves over two weeks.

Observing nerve cells rewire themselves after stroke damage.

In a technical tour de force, Winship and Murphy use the two photon imagining technique on living adult mouse brains to observe the individual neurons close to the site of damage caused by a stroke. In the first month — when paralysis is usually at its worst — they found that some neurons ditched their speciality for one particular limb and began processing information from multiple limbs. During the following month, as the affected brain region reorganized itself more permanently, those neurons re-specialized to a new single limb. Here is their abstract:

Functional mapping and microstimulation studies suggest that recovery after stroke damage can be attributed to surviving brain regions taking on the functional roles of lost tissues. Although this model is well supported by data, it is not clear how activity in single neurons is altered in relation to cortical functional maps. It is conceivable that individual surviving neurons could adopt new roles at the expense of their usual function. Alternatively, neurons that contribute to recovery may take on multiple functions and exhibit a wider repertoire of neuronal processing. In vivo two-photon calcium imaging was used in adult mice within reorganized forelimb and hindlimb somatosensory functional maps to determine how the response properties of individual neurons and glia were altered during recovery from ischemic damage over a period of 2–8 weeks. Single-cell calcium imaging revealed that the limb selectivity of individual neurons was altered during recovery from ischemia, such that neurons normally selective for a single contralateral limb processed information from multiple limbs. Altered limb selectivity was most prominent in border regions between stroke-altered forelimb and hindlimb macroscopic map representations, and peaked 1 month after the targeted insult. Two months after stroke, individual neurons near the center of reorganized functional areas became more selective for a preferred limb. These previously unreported forms of plasticity indicate that in adult animals, seemingly hardwired cortical neurons first adopt wider functional roles as they develop strategies to compensate for loss of specific sensory modalities after forms of brain damage such as stroke.

fMRI of perspective taking with robots!

Here is a quirky item... set up a human machine interaction, and as the machine is given more human-like response characteristics, parts of our brain that do 'theory of mind' (attributing intentions to others, etc.) become active. We humanize the robot. From the paper:

When our PC goes on strike again we tend to curse it as if it were a human being. Why and under which circumstances do we attribute human-like properties to machines? Although humans increasingly interact directly with machines it remains unclear whether humans implicitly attribute intentions to them and, if so, whether such interactions resemble human-human interactions on a neural level. In social cognitive neuroscience the ability to attribute intentions and desires to others is being referred to as having a Theory of Mind (ToM). With the present study we investigated whether an increase of human-likeness of interaction partners modulates the participants' ToM associated cortical activity.

...we investigated cortical activity modulation during highly interactive human-robot game. Increasing degrees of human-likeness for the game partner were introduced by means of a computer partner, a functional robot, an anthropomorphic robot and a human partner. The classical iterated prisoner's dilemma game was applied as experimental task which allowed for an implicit detection of ToM associated cortical activity...functional imaging data revealed a highly significant linear increase of cortical activity in the medial frontal cortex as well as in the right temporo-parietal junction in correspondence with the increase of human-likeness of the interaction partner...

Most popular consciousness papers

Most popular downloads for June 2008, from the ASSC archive. Also, some of the papers from the annual meeting in Taipei are here:

1. Destrebecqz, Arnaud and Peigneux, Philippe (2005) Methods for studying
unconscious learning. In: Progress in Brain Research. Elsevier, pp. 69-80.
2207 downloads from 27 countries. http://eprints.assc.caltech.edu/170/
2. Koriat, A. (2006) Metacognition and Consciousness. In: Cambridge handbook
of consciousness. Cambridge University Press, New York, USA. 1437 downloads
from 24 countries. http://eprints.assc.caltech.edu/175/
3. Dehaene, Stanislas and Changeux, Jean-Pierre and Naccache, Lionel and
Sackur, Jérôme and Sergent, Claire (2006) Conscious, preconscious, and
subliminal processing: a testable taxonomy. Trends in Cognitive Science, 10
(5). pp. 204-211. 1047 downloads from 25 countries.
http://eprints.assc.caltech.edu/20/
4. Mashour, George A. (2007) Inverse Zombies, Anesthesia Awareness, and the
Hard Problem of Unconsciousness. In: 11th Annual Meeting of the ASSC, Las
Vegas. 756 downloads from 17 countries. http://eprints.assc.caltech.edu/294/
5. Chalmers, David J. (2004) How can we construct a science of
consciousness? In: The Cognitive Neurosciences III. MIT Press, Cambridge,
MA. 714 downloads from 11 countries. http://eprints.assc.caltech.edu/28/

How we impose a natural order on events...

Goldin-Meadow et al. do interesting experiments on how speakers of different languages represent events nonverbally, finding that linguistic differences in subject-object-verb placement do not carry over into gestural depictions of the same event. (English, Chinese, and Spanish speakers typically use the order subject-verb-object to describe an event; Turkish speakers use subject-object-verb.) This suggests a natural cognitive sequence for representing events.

To test whether the language we speak influences our behavior even when we are not speaking, we asked speakers of four languages differing in their predominant word orders (English, Turkish, Spanish, and Chinese) to perform two nonverbal tasks: a communicative task (describing an event by using gesture without speech) and a noncommunicative task (reconstructing an event with pictures). We found that the word orders speakers used in their everyday speech did not influence their nonverbal behavior. Surprisingly, speakers of all four languages used the same order and on both nonverbal tasks. This order, actor–patient–act, is analogous to the subject–object–verb pattern found in many languages of the world and, importantly, in newly developing gestural languages. The findings provide evidence for a natural order that we impose on events when describing and reconstructing them nonverbally and exploit when constructing language anew.

The authors speculate:

...that, rather than being an outgrowth of communicative efficiency or the manual modality, actor-patient-act may reflect a natural sequencing for representing events. Entities are cognitively more basic and less relational than actions, which might lead participants to highlight entities involved in an action before focusing on the action itself, thus situating actor and patient before action. Moreover, there is a particularly close cognitive tie between objects and actions, which would link patient to action, resulting in an actor-patient-act order.

Mendelssohn, continued

The is the weekly posting of an portion of the house concert at Twin Valley on 6/29/08 the Molto allegro ed agitato from Mendelssohn's 1st piano trio.

The 'connectome' of our cerebral cortex

Hagmann et al. use diffusion mapping techniques to provide some awesome summary graphics of connectivity networks of our cerebral cortex. Regions of the neocortex are linked by a dense network of neural pathways, with several distinct nodes, like airline hubs. Their data:

...provides evidence for the existence of a structural core in human cerebral cortex. This complex of densely connected regions in posterior medial and parietal cortex is both spatially and topologically central within the brain. Its anatomical correspondence with regions of high metabolic activity and with some elements of the human default network suggests that the core may be an important structural basis for shaping large-scale brain dynamics. The availability of single-participant structural and functional connection maps now provides the opportunity to investigate interparticipant connectional variability and to relate it to differences in individual functional connectivity and behavior.

Click on figure to enlarge...

The Bio-Rad PCR song

Just to finish off our introduction to the brave new world of biotechnology advertising, here is the Bio-Rad PCR song. PCR, the polymerase chain reaction, is a laboratory technique used to amplify DNA that uses thermal cycling units made by Bio-Rad and others.

Ubiquity of same-sex couplings in nature.

A student has pointed out to me an interesting article in Science American Mind on unorthodox sex in the animal kingdom:

As many as 1,500 species of wild and captive animals have been observed engaging in homosexual activity. Speculations seeking an evolutionary rationale are that animals may engage in same-sex couplings to diffuse social tensions, to better protect their young or to maintain fecundity when opposite-sex partners are unavailable—or simply because it is fun. Bisexuality is a natural state among animals, perhaps Homo sapiens included, despite the sexual-orientation boundaries most people take for granted. In humans the categories of gay and straight are socially constructed.

...homosexuality among some species, including penguins, appears to be far more common in captivity than in the wild. Captivity, scientists say, may bring out gay behaviors in part because of a scarcity of opposite-sex mates. In addition, an enclosed environment boosts an animal’s stress levels, leading to a greater urge to relieve the stress. Some of the same influences may encourage what some researchers call “situational homosexuality” in humans in same-sex settings such as prisons or sports teams.

Driscoll's article continues to describe a number of studies of same-sex partners in wild and captive animals.

Buy an automatic pipette from a boy band?

I am sitting now in my office in Bock Laboratories at the University of Wisconsin, where I ran a research factory for 30 years, generating Ph.D.s, Post-Docs, and some information on how our eyes turn light into a nerve signal. (My office as a retired professor is what I call a 'view with a room', and is actually upstairs at the top of the building in which my factory occupied half the third floor.) During that period I purchased hundreds of automatic pipettes (for accurately delivering small volumes of liquid) from the Eppendorf company, ordering from a simple dry brochure, and occasionally seeing an add in a scientific magazine.

Here, then, is my latest "Oh my Gawd, how things have changed" experience. Eppendorf using a Boy Band video to advertise its product:

The relaxation response correlates with changes in gene expression

Herbert Benson's book "The Relaxation Response" which appeared about 25 years ago, has had great influence in shaping public awareness of the debilitating effects of stress and anxiety and measure that can be taken to counter it. His institute at the Mass General Hospital has generated an interesting study of changes in gene expression profiles observed in short and long term relaxation response (RR) practitioners. A bit of context is provided in the introduction:

Mind-body approaches that elicit the RR include: various forms of meditation, repetitive prayer, yoga, tai chi, breathing exercises, progressive muscle relaxation, biofeedback, guided imagery and Qi Gong. One way that the RR can be elicited is when individuals repeat a word, sound, phrase, prayer or focus on their breathing with a disregard of intrusive everyday thoughts. The non-pharmacological benefit of the RR on stress reduction and other physiological as well as pathological parameters has attracted significant interest in recent years to decipher the physiological effects of the RR. In addition to decreased oxygen consumption, other consistent physiologic changes observed in long-term practitioners of RR techniques include decreased carbon dioxide elimination, reduced blood pressure, heart and respiration rate, prominent low frequency heart rate oscillations and alterations in cortical and subcortical brain regions.

The authors observed changes in gene expression profiles regulating molecular and biochemical pathways involved in cellular metabolism, oxidative phosphorylation, generation of reactive oxygen species and response to oxidative stress. They suggest that these changes to some degree serve to ameliorate the negative impact of stress (which is known to increase oxidative stress and promote a pro-inflammatory milieu).

Chopin's Heart

A quirky item that I pass on since I am a Chopin fanatic...From the "Random Samples" section of the 11 July issue of Science:

Frédéric Chopin died in France in 1849 at the age of 39 of what his death certificate recorded as "tuberculosis of the lungs and larynx." After his death, friends had the composer's heart removed, submerged in a jar of cognac, and placed in a Warsaw church in his native Poland in accordance with his wishes.

Now Polish scientists want to reopen the jar to see whether Chopin actually died of cystic fibrosis. Michal Witt of Warsaw's International Institute of Molecular and Cell Biology has argued that Chopin had childhood symptoms matching a mild form of the genetic illness, including respiratory infections, weakness, and delayed puberty. As an adult, Chopin was slight of stature, had a hard time climbing stairs, and occasionally had to be carried offstage after concerts. "If it turned out that Chopin had cystic fibrosis, this would be very special news for all those affected with CF," Witt says.

Witt hopes to persuade Polish authorities to open the niche where Chopin's heart is stored by 2010, the 200th anniversary of his birth. "It's a good moment to check, and once we have it in our hands it's a small matter to do a CT [computed tomography] scan and DNA test," says Tadeusz Dobosz, a geneticist at Wroc aw Medical University. Poland's Culture Ministry is considering the request.

Persistence of anxious temperament - brain correlates

The temperament we display in early childhood (introvesion versus extroversion, high versus low reactivity, anxiety in unfamiliar versus familiar situations, etc) is largely genetically determined and persists through life. The work of Kagan and others has shown that children classed as highly reactive as babies are more likely to be subdued in unfamiliar situations and report a dour mood and anxiety over the future. Anxious temperament is an early predictor of the later risk to develop anxiety, depression and drug abuse related to self-medicating. It becomes increasingly clear that people with anxious temperaments are come wired that way, telling them to calm down just doesn't work. Kalin and his colleagues here at Wisconsin have produced an interesting study on the relevant brain correlates of this behavior by looking at brain activity, anxious behavior and stress hormones in adolescent rhesus monkeys, which have been used in numerous studies as models to understand anxious temperament in human children. They found that individuals with the most anxious temperaments showed higher activity in the amygdala, which regulates emotion and triggers reactions to anxiety, such as the fight or flight response. These anxious monkeys had more metabolic activity in the amygdala in both secure and threatening situations. These differences remained over several years of testing. From their abstract:

Regardless of context, results demonstrated a trait-like pattern of brain activity (amygdala, bed nucleus of stria terminalis, hippocampus, and periaqueductal gray) that is predictive of individual phenotypic differences. Importantly, individuals with extreme anxious temperament also displayed increased activity of this circuit when assessed in the security of their home environment. These findings suggest that increased activity of this circuit early in life mediates the childhood temperamental risk to develop anxiety and depression. In addition, the findings provide an explanation for why individuals with anxious temperament have difficulty relaxing in environments that others perceive as non-stressful.

Self interest versus 'moral sentiment' in economic policy

A review by Bowles in Science considers:

...a shortcoming in the conventional economic approach to policy design: It overlooks the possibility that economic incentives that appeal to self interest may diminish ethical or other reasons for complying with social norms and contributing to the common good. It cites one simple example of this happening:

In Haifa, at six day care centers, a fine was imposed on parents who were late picking up their children at the end of the day. Parents responded to the fine by doubling the fraction of time they arrived late. When after 12 weeks the fine was revoked, their enhanced tardiness persisted unabated. While other interpretations are possible, the counterproductive imposition of the fines illustrate a kind of negative synergy between economic incentives and moral behavior. The fine seems to have undermined the parents' sense of ethical obligation to avoid inconveniencing the teachers and led them to think of lateness as just another commodity they could purchase.

A clip from the Bowles' discussion:

Although standard in economics, reliance solely on self-interest in the design of policies has never won universal assent. Until recently, however, dissenting views, like Titmuss' celebrated claim that paying for blood donations degrades the willingness to contribute, were thought to lack either empirical support or a coherent account of why separability might fail. But a recent experiment suggests that Titmuss may have been right, at least for women. Other experiments surveyed in this review provide additional evidence that material interests and moral sentiments are not separable in the sense required by the conventional economic approach to policy-making.

Economists, psychologists, and others, in part stimulated by these new empirical data, are well on their way to constructing an economic psychology of the interplay of self-regarding and other-regarding motivation that may eventually enlighten mechanism design and public policy....Good policies and constitutions are those that support socially valued ends not only by harnessing selfish preferences to public ends but also by evoking, cultivating, and empowering public-spirited motives. The modest tax on plastic grocery bags enacted in Ireland in 2002 that resulted in a 94 per cent decline in their use appears to have had just this effect : Carrying a plastic bag joined wearing a fur coat in the gallery of antisocial anachronisms.

Mendelssohn piano trios....

The is the first of what will be several weekly postings of portions of the house concert at Twin Valley on 6/29/08. This is the Andante con moto tranquillo from Mendelssohn's 1st piano trio. I am playingon the Steinway B, with Sonny Enslen (cello) and Daphne Tsao (violin).

The choices you make - indirect social influence.

I thought I was pass on this brief perspectives essay from Science by Jerker Denrell:

To what extent are the opinions you hold simply a reflection of the opinions of those you associate with? Most people like to think that their opinions are based on their own deliberations. Of course, there are exceptions. You may take into account the opinions of others if you believe they are better informed. You may even conform to the majority opinion in order to avoid being seen as deviant (1, 2). Studies of how norms and beliefs vary between groups, and how they are transmitted from peers or parents, testify to the importance of such social influence (3).

Explanations of social influence usually focus on why people are persuaded by or conform to the opinions of others (4). Although important, this research has neglected the role of information collection in belief formation and how biased beliefs, as well as social influence, can emerge from biased search processes (5).

For example, suppose you are deciding which of two cars to buy. If your neighbor buys one of the cars, you can observe it more closely and will thus learn more about its attributes. This opportunity to observe the car can bias your decision toward buying the same car, even if you do not care about whether you have the same car as your neighbor. This is especially true if acquiring information about cars other than your neighbor's is costly (6). If the information you learn about your neighbor's car is strongly positive, it makes sense to buy this car and discontinue the search. In this case you will not find out whether the other car is superior. If the information you learn is not very positive, however, it then makes sense to examine the other car. Only in this case will you find out how the two cars compare. Because the comparison process is asymmetric, you are overall more likely to buy the same car as your neighbor even if the information you learn is equally likely to be positive or negative.

The attitudes and behavior of others can also influence our learning processes by leading us to revisit objects and events that we had previously avoided because of poor past experiences (7). Suppose Bob likes a restaurant while Alice does not. By herself Alice might not visit the restaurant again, and her attitude would remain negative. But Alice might join Bob if he wants to go to the restaurant. By visiting the restaurant again, Alice gets a chance to change her opinion. Alice's attitude will depend on Bob's, but only because he influenced the probability of her revisiting the restaurant.

Finally, the number of your friends who engage in some activity can also influence your estimate of the value of this activity. If you have many friends who start firms, for example, your estimate of the chances of success will be based on a large sample size. A large sample size may lead you to have a higher estimate of the success rate than you would if the sample size were small. Experiments show that a large sample size leads to a more optimistic view when the outcome distribution is skewed (8). If only 10% succeed, you may only observe failures in a small sample, and will then underestimate the success rate.

These mechanisms produce behavior that looks like conformity: You are more likely to evaluate an activity positively if others do so. But in these examples your attitude is not directly influenced by hearing about the attitudes of others. Your attitude is only indirectly influenced by others because their behavior exposes you to additional samples of the activity.

Such indirect mechanisms of social influence are important, because even individuals who try to be impartial and make the best decision given the available information may fail to recognize that the available information is influenced by others (9). For example, a manager who tries to avoid discrimination may nevertheless come to believe that individuals who belong to the same social networks as the manager does are superior to those the manager seldom interacts with and has less information about. To learn more about these mechanisms, we need to broaden studies of social influence and belief formation to include the phases of learning and information collection that precede decision-making and judgment (10).

References and Notes

1. S. E. Asch, Sci. Am. 193, 31 (November, 1955).
2. M. Deutsch, H. Gerard, J. Abnorm. Soc. Psychol. 51, 629 (1955).
3. P. J. Richerson, R. Boyd, Not by Genes Alone: How Culture Transformed Human Evolution (Univ. of Chicago Press, Chicago, 2005).
4. R. B. Cialdini, N. J. Goldstein, Annu. Rev. Psychol. 55, 591 (2004).
5. Y. Trope, A. Liberman, in Social Psychology: Handbook of Basic Principles, E. T. Higgins, A. W. Kruglanski, Eds. (Guilford, New York, 1996), pp. 239-270.
6. N. V. Moshkin, R. Shachar, Market. Sci. 21, 435 (2002).
7. J. Denrell, G. Le Mens, Psychol. Rev. 114, 398 (2007).
8. R. Hertwig et al., Psychol. Sci. 15, 534 (2004).
9. J. Denrell, Psychol. Rev. 112, 951 (2005).
10. For recent research on the effect of sampling on judgment, see K. Fiedler, P. Juslin, Eds., Information Sampling and Adaptive Cognition (Cambridge Univ. Press, Cambridge, 2006).

Resveratrol - protection from ravages of aging.

In mice, at least....An article in Wired Magazine points to a multi-authored study in Cell Metabolism:

A small molecule that safely mimics the ability of dietary restriction (DR) to delay age-related diseases in laboratory animals is greatly sought after. We and others have shown that resveratrol mimics effects of DR in lower organisms. In mice, we find that resveratrol induces gene expression patterns in multiple tissues that parallel those induced by DR and every-other-day feeding. Moreover, resveratrol-fed elderly mice show a marked reduction in signs of aging, including reduced albuminuria, decreased inflammation, and apoptosis in the vascular endothelium, increased aortic elasticity, greater motor coordination, reduced cataract formation, and preserved bone mineral density. However, mice fed a standard diet did not live longer when treated with resveratrol beginning at 12 months of age. Our findings indicate that resveratrol treatment has a range of beneficial effects in mice but does not increase the longevity of ad libitum-fed animals when started midlife.

Where Ritalin acts in the brain to focus attention.

An interesting piece of work from Berridge's lab here at the University of Wisconsin shows that the cognition and attention enhancing drug Ritalin (methylphenidate, MPH) fine-tunes the functioning of neurons in the prefrontal cortex (PFC), which is involved in attention, decision-making and impulse control. While it enhances the efflux of the neurotransmitters norepinephrine and dopamine in PFC, it appears to have minimal effects elsewhere.

Only working memory–enhancing doses of MPH increased the responsivity of individual PFC neurons and altered neuronal ensemble responses within the PFC. The effects were not observed outside the PFC (i.e., within somatosensory cortex). In contrast, high-dose MPH profoundly suppressed evoked discharge of PFC neurons. These observations suggest that preferential enhancement of signal processing within the PFC, including alterations in the discharge properties of individual PFC neurons and PFC neuronal ensembles, underlie the behavioral/cognitive actions of low-dose psychostimulants.

As new kind of science, as data deluge makes the scientific method obsolete...

An article by Chris Anderson in Wired Magazine, pointed out to me by my son Jon, argues that science as we have known it has ended. The argument is that the quest for knowledge that used to begin with grand theories now, in the petabyte age, begins with massive amounts of data. Google has set the new model for science. I show some clips here, and then follow with the contra argument by John Timmers that follows):

Google conquered the advertising world with nothing more than applied mathematics. It didn't pretend to know anything about the culture and conventions of advertising — it just assumed that better data, with better analytical tools, would win the day. And Google was right...Google's founding philosophy is that we don't know why this page is better than that one: If the statistics of incoming links say it is, that's good enough. No semantic or causal analysis is required. That's why Google can translate languages without actually "knowing" them (given equal corpus data, Google can translate Klingon into Farsi as easily as it can translate French into German). And why it can match ads to content without any knowledge or assumptions about the ads or the content.

The hypothesize-model-test model of science is becoming obsolete...The models we were taught in school about "dominant" and "recessive" genes steering a strictly Mendelian process have turned out to be an even greater simplification of reality than Newton's laws. The discovery of gene-protein interactions and other aspects of epigenetics has challenged the view of DNA as destiny and even introduced evidence that environment can influence inheritable traits, something once considered a genetic impossibility...the more we learn about biology, the further we find ourselves from a model that can explain it...There is now a better way. Petabytes allow us to say: "Correlation is enough." We can stop looking for models. We can analyze the data without hypotheses about what it might show. We can throw the numbers into the biggest computing clusters the world has ever seen and let statistical algorithms find patterns where science cannot.

The best practical example of this is the shotgun gene sequencing by J. Craig Venter. Enabled by high-speed sequencers and supercomputers that statistically analyze the data they produce, Venter went from sequencing individual organisms to sequencing entire ecosystems. In 2003, he started sequencing much of the ocean, retracing the voyage of Captain Cook. And in 2005 he started sequencing the air. In the process, he discovered thousands of previously unknown species of bacteria and other life-forms.

Venter can make some guesses about the animals — that they convert sunlight into energy in a particular way, or that they descended from a common ancestor. But besides that, he has no better model of this species than Google has of your MySpace page. It's just data. By analyzing it with Google-quality computing resources, though, Venter has advanced biology more than anyone else of his generation.

This kind of thinking is poised to go mainstream. In February, the National Science Foundation announced the Cluster Exploratory, a program that funds research designed to run on a large-scale distributed computing platform developed by Google and IBM in conjunction with six pilot universities. The cluster will consist of 1,600 processors, several terabytes of memory, and hundreds of terabytes of storage, along with the software, including Google File System, IBM's Tivoli, and an open source version of Google's MapReduce. Early CluE projects will include simulations of the brain and the nervous system and other biological research that lies somewhere between wetware and software.

Here is the immediate rejoinder to this article from John Timmers at Ars Technica.

Every so often, someone (generally not a practicing scientist) suggests that it's time to replace science with something better. The desire often seems to be a product of either an exaggerated sense of the potential of new approaches, or a lack of understanding of what's actually going on in the world of science. This week's version, which comes courtesy of Chris Anderson, the Editor-in-Chief of Wired, manages to combine both of these features in suggesting that the advent of a cloud of scientific data may free us from the need to use the standard scientific method.

It's easy to see what has Anderson enthused. Modern scientific data sets are increasingly large, comprehensive, and electronic. Things like genome sequences tell us all there is to know about the DNA present in an organism's cells, while DNA chip experiments can determine every gene that's expressed by that cell. That data's also publicly available—out in the cloud, in the current parlance—and it's being mined successfully. That mining extends beyond traditional biological data, too, as projects like WikiProteins are also drawing on text-mining of the electronic scientific literature to suggest connections among biological activities.

There is a lot to like about these trends, and little reason not to be enthused about them. They hold the potential to suggest new avenues of research that scientists wouldn't have identified based on their own analysis of the data. But Anderson appears to take the position that the new research part of the equation has become superfluous; simply having a good algorithm that recognizes the correlation is enough.

The source of this flight of fancy was apparently a quote by Google's research director, who repurposed a cliché that most scientists are aware of: "All models are wrong, and increasingly you can succeed without them." And Google clearly has. It doesn't need to develop a theory as to why a given pattern of links can serve as an indication of valuable information; all it needs to know is that an algorithm that recognizes specific link patterns satisfies its users. Anderson's argument distills down to the suggestion that science can operate on the same level—mechanisms, models, and theories are all dispensable as long as something can pick the correlations out of masses of data.

Science 2.0 I can't possibly imagine how he comes to that conclusion. Correlations are a way of catching a scientist's attention, but the models and mechanisms that explain them are how we make the predictions that not only advance science, but generate practical applications. One only needs to look at a promising field that lacks a strong theoretical foundation—high-temperature superconductivity springs to mind—to see how badly the lack of a theory can impact progress. Put in more practical terms, would Anderson be willing to help test a drug that was based on a poorly understood correlation pulled out of a datamine? These days, we like our drugs to have known targets and mechanisms of action and, to get there, we need standard science.

Anderson does provide two examples that he feels support his position, but they actually appear to undercut it. He notes that we know quantum mechanics is wrong on some level, but have been unable to craft a replacement theory after decades of work. But he neglects to mention two key things: without the testable predictions made by the theory, we'll never be able to tell how precisely it is wrong and, in those decades where we've failed to find a replacement, the predictions of quantum mechanics have been used to create the modern electronics industry, with the data cloud being a consequence of that.

If anything, his second example is worse. We can now perform large-scale genetic surveys of the life present in remote environments, such as the far reaches of the Pacific. Doing so has informed us that there's a lot of unexplored biodiversity on the bacterial level; fragments of sequence hint at organisms we've never encountered under a microscope. But as Anderson himself notes, the only thing we can do is make a few guesses as to the properties of the organisms based on who their relatives are, an activity that actually requires a working scientific theory, namely evolution. To do more than that, we need to deploy models of metabolism and ecology against the bacteria themselves.

Overall, the foundation of the argument for a replacement for science is correct: the data cloud is changing science, and leaving us in many cases with a Google-level understanding of the connections between things. Where Anderson stumbles is in his conclusions about what this means for science. The fact is that we couldn't have even reached this Google-level understanding without the models and mechanisms that he suggests are doomed to irrelevance. But, more importantly, nobody, including Anderson himself if he had thought about it, should be happy with stopping at this level of understanding of the natural world.

Meditation and executive function - untraining the brain.

A MindBlog reader passes on this link to a reposting of a interesting article by Chris Chatham on how easily normal conflicts in making decisions can be lessened by changes in attention. My May 1 post references other work on this topic.