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An Eagle of Cosmic Proportions

Friday, August 28, 2009

An Eagle of Cosmic Proportions (7/16/09)
Located 7000 light-years away, towards the constellation of Serpens (the Snake), the Eagle Nebula is a dazzling stellar nursery, a region of gas and dust where young stars are currently being formed and where a cluster of massive, hot stars, NGC 6611, has just been born. The powerful light and strong winds from these massive new arrivals are shaping light-year long pillars, seen in the image partly silhouetted against the bright background of the nebula. The nebula itself has a shape vaguely reminiscent of an eagle, with the central pillars being the “talons”.

Eagle Neblula – click for 1280×1280 image

Atrocious science writer clichés

Sunday, August 23, 2009

Wired's Betsy Mason, who plainly has better taste and better sense than the average science writer, has an entertaining list of

5 Atrocious Science Clichés to Throw Down a Black Hole
A black hole is the perfect place for stuff you never want to see again. So Wired Science is joining Wired.com’s extended black hole party by chucking in some of the worst, most overused science clichés.

I heartily endorse all of her picks, especially the first three. Online comments to the article add a number of other choice clunkers.

In that spirit, I'll add a few of my own.

  • atom smasher – actual atom smashers largely ceased to be big news in the 1950s or so, shortly before they were superseded by particle accelerators, like the Stanford Linear Accelerator (1966), designed to smash the constituent subatomic particles of atoms
  • god particle – nauseating term for the Higgs boson, designed to appeal to the religiously obsessed by people who really should know better; New York Times writer Dennis Overbye actually covered himself in... well, something, when he attempted to defend this merde, instead of casting it into the outer darkness
  • black hole machine – a popular circumlocution used by writers who seize up at the thought of using the proper name Large Hadron Collider, based most unfortunately on the widely circulated nonsense about the possibility a microscopic black hole created by the LHC might destroy the universe (a feat that, in spite of much to be said in its favor, even black holes a billion times more massive than our sun are incapable of)
  • pave the way – a hoary metaphor that must date from the days of Telford and McAdam, if not the Romans and their roads; it's now full of potholes, and most commonly used to refer to some scientific finding of no great importance at present, but for which its discoverers are hopeful of being recognized at some indefinite time in the future
  • groundbreaking – another construction metaphor equally as odoriferous, and inane, as "paving the way"
  • breakthrough – what some writers call a scientific finding, just before they say it "paves the way"
  • a possible cure for _____ – a way to describe a biomedical discovery that will probably also be described as "groundbreaking" or "a breakthrough", even though the odds are heavily against it leading to a cure for anything
  • shed light on – listed by Betsy also, but so awful it needs to be repeated in this list. (Added 10/15/09: see this for an egregious example that combines, in the title and first two paragraphs, the last three types of atrociousness.)
  • guardian of the genome – what writers who are too cowardly to write "p53" use for the name of said protein and its gene, apparently because they think that the public appreciates authoritarian metaphors
  • Lou Gehrig's disease – a neurological disease whose proper name is amyotrophic lateral sclerosis, named after some American athletic dude of the 1930s who's mostly remembered now for having contracted the disease; also referred to by Brits as "motor neurone disease" when, if they had any sense, they'd call it Stephen Hawking's disease
  • key to unlocking the mystery – as if scientific "secrets" are highly classified memoranda or cabalistic esoterica kept under lock and key... I suppose this sort of thing appeals to detective story fans and conspiracy theorists; great for promoting science as a form of infotainment, but a cliché nevertheless, as is most of the genre it's based on; this cliché is akin to "paving the way", because it's useful for describing results that fall short of resolving a question

Inflammation, microRNA, and cancer

Sunday, August 16, 2009

If there's just one single point worth making about the biology of cancer, it would have to be "it's complicated".

Cells in general, and animal cells in particular, are extremely intricate Rube-Goldberg-like mechanisms. Their correct functioning depends on the integrity of 20,000 or so genes (in the case of humans), and at least 5 times as many proteins whose form is specified by the genes. Damage to even one of a few thousand important genes can put a cell on the road to becoming cancerous. So the first fact about cancer isn't really all that hard to understand: cancer (in all of its many forms) is a disease that begins with damage to the DNA of one or more genes.

This damage, which is necessary but not sufficient, can occur in many ways. Sometimes it happens because of the action of external agents, like carcinogenic chemicals or high-energy radiation (including ultraviolet light). Other times it happens simply because of occasional errors made in copying DNA during the process of cell division. These are just a few of many ways in which DNA can suffer damage. It's estimated that from 10,000 to a million DNA mutations can occur in a single human cell per day.

Fortunately, only a few percent of the 3 billion fundamental units (base pairs) of DNA actually occur within genes – everything else is "noncoding DNA". Although much of this noncoding DNA serves some useful purpose, we have little idea at present what that might be. However, it's certainly less critical to cell function than the DNA of actual genes. Even so, 10,000 or so genes in every cell could suffer mutations every day.

Of course, complex multicellular life couldn't exist unless nature had evolved some means for coping with all this random genetic damage. And so, there are a large number of ways that cells have of detecting and repairing the damage that does occur. Then in the relatively small number of cases where damage cannot be repaired, cells have additional fail-safe mechanisms to avoid malfunctions which lead to unlimited proliferation – i. e. cancer. One such mechanism is for a cell to enter a state of "senescence", where it ceases to be able to divide at all. A more drastic, but common, mechanism is for the cell to undergo "apoptosis" – orderly cell death.

A necessary condition, therefore, for a cell to become cancerous, even after DNA damage remains unrepaired (perhaps because of damage to part of the repair mechanism), is that the damage occurs in a gene that codes for proteins needed for one of the various fail-safe mechanisms. Consequently, in almost every case of cancer where a tumor has begun to form, one finds problems in some part of the cell's anti-proliferation machinery.

We'll look at a recent piece of research that identifies one particular way this can happen, and it's interesting for the variety of different cell processes that become involved.

Many of the known "causes" of cancer are fairly easy to understand. Certainly, the cancer risk from DNA-damaging carcinogenic chemicals is obvious enough. And once one understands how important a key protein known as p53 is in crucial cellular processes such as detection of unrepaired DNA damage and invocation of apoptosis if necessary, it's not hard to understand why more than 50% of human tumors have mutated genes for p53.

But there are other factors which have been found, in epidemiological studies, to be statistically associated with cancer development. One of these is inflammation, which is a very normal part of the body's immunological defenses against infection. Inflammation itself is a highly complex process – too complex to outline here. Chronic infections by various agents can cause a state of persistent inflammation. An example is the result of H. pylori bacterial infections. In addition to being responsible for stomach ulcers, such infections are also found in cases of stomach cancer. Obesity is also known as an epidemiological factor in various cancers, and the reason is now thought to be the state of chronic inflammation that obesity often causes.

What is not clear is exactly what mechanism connects inflammation with cancer. There's undoubtedly a variety of mechanisms, given how complicated cellular processes turn out to be when you get down to the finer details. The recent research mentioned above illustrated one such mechanism, in one single type of cancer.

Anti-inflammatory drugs may defeat a treatment-resistant type of cancer (6/24/09)
The research focused on a type of non-Hodgkin lymphoma called diffuse large B-cell lymphoma. In some patients with the disease, chemotherapy works well. In a recent study of 40 patients more than 75 percent of patients with one form of this type of lymphoma survived five years or longer.

But that study also identified a group of patients whose cancer proved difficult to treat. Their tumors failed to respond to chemotherapy, and only 16 percent of patients with this form of lymphoma survived more than five years after they were diagnosed.

Several molecular flags mark this treatment-resistant lymphoma, but the links between them were unknown until now. The new paper reports that tumor cells isolated from these patients have depressed levels of a protein called SHIP1, which was known to suppress tumors. In fact, patients with the lowest levels of SHIP1 are the least likely to survive.

SHIP1 is a phosphatase enzyme. That means it removes phosphate groups from proteins. So a phosphatase has the opposite effect of enzymes known as kinases, which attach phosphate groups to proteins. Having a phosphate group attached at the right place on a protein is what enables the protein to take part in a signaling pathway, which is the basic communication mechanism in a cell responsible for making things happen. Therefore, phosphatases disrupt pathways, and stop things from happening. This can be beneficial, for example, if what's happening is the excessive cell division that occurs in cancer. Accordingly, SHIP1 has been found to be a tumor suppressing protein.

In the case of diffuse large B-cell lymphoma (DLBCL), it is found that SHIP1 levels are abnormally low. It's not that the SHIP1 is defective; there's just not enough of it. So the question is why. Is there some other defective gene that's responsible?

Apparently, there is not. Instead, it's the presence of inflammation that's responsible, and in an interesting way. Inflammation is a perfectly normal product of the body's immune system, and it exists to counteract harmful agents such as bacteria. The immune system initiates and regulates the process of inflammation by means of signaling molecules called cytokines. One of the more common and important of these cytokines is TNFα.

Now, TNFα normally goes about its business without causing cancer or other lasting ill effects. In fact, under the right conditions it can induce apoptosis or inhibit tumor formation in other ways. But for some reason, in DLBCL, TNFα suppresses SHIP1, and thus promotes cancer. The research in question also discovered the mechanism of SHIP1 suppression. It turns out that the real culprit here is a small piece of microRNA called miR-155. This little bugger was already known to be involved with leukemia in mice, and with other cancers. (See references in here.)
The resistant type of lymphoma cells also have elevated levels of miR-155, a specific example of a type of genetic material called microRNA, the team found. They demonstrated that miR-155 suppresses SHIP1 by sticking to the template for the protein, preventing its manufacture. ...

The final clue came from earlier reports that an inflammatory molecule called TNFα could boost levels of miR-155. Additional laboratory work confirmed the observation for this type of lymphoma cell.

Some anti-inflammatory drugs, used for diseases such as arthritis and inflammatory bowel disease, where inflammation gets out of hand, work by suppressing TNFα. So it was hypothesized that such a drug might be beneficial in treating DLBCL. And voilà:
The anti-inflammatory drugs etanercept and infliximab, which are currently used to treat arthritis and inflammatory bowel disease, work by suppressing TNFα, suggesting a new way to curb the malignancy of this type of lymphoma.

The team tested the idea in mice that had been injected with aggressive lymphoma cells and found that nascent tumors shrank in six days.

However, mice are not humans, so the drugs need to be tested in human DLBCL patients. Patients are already being recruited for clinical studies.

Now, there are plenty of questions remaining. More needs to be understood about just what pathways SHIP1 disrupts in order to suppress tumors. This should also help in understanding why inflammation and the resulting TNFα do not, fortunately, cause cancer more often. Baby steps. But perhaps significant ones.

Here's the research abstract:

Onco-miR-155 targets SHIP1 to promote TNFα-dependent growth of B cell lymphomas
Non-coding microRNAs (miRs) are a vital component of post-transcriptional modulation of protein expression and, like coding mRNAs harbour oncogenic properties. However, the mechanisms governing miR expression and the identity of the affected transcripts remain poorly understood. Here we identify the inositol phosphatase SHIP1 as a bonafide target of the oncogenic miR-155. We demonstrate that in diffuse large B cell lymphoma (DLBCL) elevated levels of miR-155, and consequent diminished SHIP1 expression are the result of autocrine stimulation by the pro-inflammatory cytokine tumour necrosis factor alpha (TNFα). Anti-TNFα regimen such as eternacept or infliximab were sufficient to reduce miR-155 levels and restored SHIP1 expression in DLBCL cells with an accompanying reduction in cell proliferation. Furthermore, we observed a substantial decrease in tumour burden in DLBCL xenografts in response to eternacept. These findings strongly support the concept that cytokine-regulated miRs can function as a crucial link between inflammation and cancer, and illustrate the feasibility of anti-TNFα therapy as a novel and immediately accessible (co)treatment for DLBCL.

Pedersen, I., Otero, D., Kao, E., Miletic, A., Hother, C., Ralfkiaer, E., Rickert, R., Gronbaek, K., & David, M. (2009). Onco-miR-155 targets SHIP1 to promote TNFα-dependent growth of B cell lymphomas EMBO Molecular Medicine, 1 (5), 288-295 DOI: 10.1002/emmm.200900028

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Cancer and Wnt signaling

We've discussed the Wnt signaling pathway several times before, most extensively here. The pathway involves a variety of proteins and their corresponding genes.

Wnt signaling is especially important in embryonic development. In fact, the name is derived from the name of a gene in fruit files that, when mutated, results in wingless flies.

Wnt signaling is also important in stem cells (see here, here, here). As a special case, Wnt is involved in cancer stem cells (see here).

It is far from clear that cancer stem cells are an important factor in many types of cancer. But it appears that Wnt signaling does sometimes play a role itself. Wnt has been found to assist metastasis of colon cancer, and new research suggests it also helps lung cancer to spread quickly to bones and the brain.

Research reveals what drives lung cancer's spread (7/2/09)
Researchers discovered that the same cellular pathway that has been shown to be involved with the spread of colorectal cancer is also responsible for providing lung cancer with an enhanced ability to infiltrate and colonize other organs without delay and with little need to adapt to its new environment. This is a dramatic departure from other cancers, like breast cancer, in which recurrences tend to emerge following years of remission, suggesting that such cancer cells initially lack - and need time to acquire - the characteristics and ability to spread to other organs.

The investigators hypothesized that because not all lung tumors have spread before diagnosis and removal, metastasis may depend on some added feature beyond the mutations that initiate these tumors.

Researchers used bioinformatics to interrogate large collections of lung tumor samples. They found that the WNT cell-signaling pathway was the only one out of the six pathways tested that was hyperactive in lung tumors that went on to metastasize and was normal in those that did not spread. They also observed that WNT hyperactivity was associated with aggressive biological tumor characteristics and poor clinical outcome, suggesting that cancer metastasis is linked to poor survival.

Other research groups, only a few months ago, had found evidence of Wnt involvement in a type of brain cancer, though not one due to metastasis from another location.

Study finds biological clue in brain tumour development (3/18/09)
Clinician -scientists at the University's Children's Brain Tumour Research Centre, working on behalf of the Children's Cancer and Leukaemia Group (CCLG), have studied the role of the WNT biological pathway in central nervous system primitive neuroectodermal tumours (CNS PNET), a type of brain tumour that predominantly occurs in children and presently has a very poor prognosis.

In a paper published in the British Journal of Cancer, they have shown that in over one-third of cases, the pathway is 'activated', suggesting that it plays a role in tumour development. The research also highlighted a link between WNT pathway activation and patient survival — patients who had a CNS PNET tumour that was activated survived for longer than those without pathway activation.

The reason for the link between WNT pathway activation and better patient prognosis is as yet unclear. It could be that these tumours represent a less aggressive subset or that pathway activation itself actually harms the tumour.

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Stephan's Quintet : A Galaxy Collision in Action

Wednesday, August 12, 2009

Stephan's Quintet : A Galaxy Collision in Action
This beautiful image gives a new look at Stephan's Quintet, a compact group of galaxies discovered about 130 years ago and located about 280 million light years from Earth. The curved, light blue ridge running down the center of the image shows X-ray data from the Chandra X-ray Observatory. Four of the galaxies in the group are visible in the optical image (yellow, red, white and blue) from the Canada-France-Hawaii Telescope. ... The galaxy NGC 7318b is passing through the core of galaxies at almost 2 million miles per hour, and is thought to be causing the ridge of X-ray emission by generating a shock wave that heats the gas.

Stephan's Quintet – click for 764×559 image

More: here, here

How does language shape the way we think?

A more hypothesis-free question might be "Does language shape the way we think?"

This question, in fact, goes back a long way. It can be traced to the European romantic period of the early 19th century, with antecedents that are much earlier.

But a more modern form of the question is well-known to many as the Whorfian Hypothesis or the Sapir-Whorf Hypothesis. In even more modern terminology, this is the question of linguistic relativity. (That Wikipedia article gives a fairly detailed summary.)

There's a recent essay at Edge by neuroscientist Lera Boroditsky that outlines a number of the issues and gives an entertaining account of simple experiments that have been performed to test various linguistic relativity hypotheses.

How does language shape the way we think?
Humans communicate with one another using a dazzling array of languages, each differing from the next in innumerable ways. Do the languages we speak shape the way we see the world, the way we think, and the way we live our lives? Do people who speak different languages think differently simply because they speak different languages? Does learning new languages change the way you think? Do polyglots think differently when speaking different languages?

These questions touch on nearly all of the major controversies in the study of mind. They have engaged scores of philosophers, anthropologists, linguists, and psychologists, and they have important implications for politics, law, and religion. Yet despite nearly constant attention and debate, very little empirical work was done on these questions until recently. For a long time, the idea that language might shape thought was considered at best untestable and more often simply wrong. Research in my labs at Stanford University and at MIT has helped reopen this question. We have collected data around the world: from China, Greece, Chile, Indonesia, Russia, and Aboriginal Australia. What we have learned is that people who speak different languages do indeed think differently and that even flukes of grammar can profoundly affect how we see the world.

Let's first review the history of linguistic relativity. In romantic thought during the early 19th century in Germany language was seen as expressing the "spirit" of a nation. Implicitly, then, there was a close connection between language and the social and political attitudes of a place. However, the direction of a causal link, if any, was not clearly articulated. If anything, one could infer that society and culture affect language more than the reverse.

This might have been true before the invention of writing, but since then, language generally changes much more slowly than social attitudes. Instead of following culture, one might expect language to be one of the ways that attitudes are transmitted from generation to generation. So the natural expectation now is for language to causally affect society.

Some of the assertions in Ludwig Wittgenstein's Tractatus Logico-Philosophicus (TLP) tend to support the notion that language strongly affects thought. TLP was published in 1921 and belongs to the "early period" of Wittgenstein's thought. In his later period, represented in the posthumously published Philosophical Investigations (1953), he reversed course on a number of issues. Yet many people still regard much of TLP as powerfully insightful.

The basic thrust is that one's language places limits on what can usefully be thought, especially: "The limits of my language mean the limits of my world." (TLP, 5.6) And the concluding assertion of the book: "Whereof one cannot speak, thereof one must be silent." (TLP, 7) One interpretation is that although one might have certain thoughts one can't express in language, such thoughts would be largely futile, since they could not be communicated to others (at least not verbally) or even to oneself at a later time – perhaps only hours or even minutes later. At all events, limitations on the expressive power of a particular language place constraints on useful thinking. (To a large extent, this should be an empirical question about how much the brain uses a natural language to help with long-term storage of abstract thoughts. It seems very plausible – we need only recall a short aphorism like Wittgenstein's to access the more complex ideas. In fact, there's now a common term for this: "sound bites".)

A century after the German romantics, Edward Sapir (1884-1939), an American anthropologist and linguist, began to put the study of the relationship between language and thought on a more systematic and scientific basis. Sapir's linguistic studies adopted an anthropological approach (under the influence of Franz Boas), including field work exploring native American languages.

Although Sapir's connection with the question of a relationship between language and thought becomes more explicit in the work and writings of his student, Benjamin Lee Whorf, Sapir himself did much to encourage examination of the relationship. His introductory book on linguistics, Language: An Introduction to the Study of Speech is still in print. In Chapter X of it he wrote "Nor can I believe that culture and language are in any true sense causally related." But nevertheless, "Language and our thought-grooves are inextricably interrelated, are, in a sense, one and the same."

Benjamin Lee Whorf (1897-1941) was much more closely identified with the question, so much so that the idea of an influence of language on thought is often called simply the Whorfian Hypothesis. His collection of writings, still in print, Language, Thought, and Reality, is the work for which he is best known. Representative quote:
We dissect nature along lines laid down by our native language. The categories and types that we isolate from the world of phenomena we do not find there because they stare every observer in the face; on the contrary, the world is presented in a kaleidoscope flux of impressions which has to be organized by our minds—and this means largely by the linguistic systems of our minds.

For some time more recently, especially in the 1980s, the Whorfian Hypothesis (which wasn't actually stated explicitly by Whorf) and the idea of linguistic relativity in general was not well regarded by cognitive scientists, because it lacked precision, testable hypotheses, and (consequently) experimental evidence. It was, after all, largely speculations based on anthropological observations. Lack of experimental evidence made a skeptical view of linguistic relativity easier to hold. But since the 1990s many attempts have been made to study the question scientifically and experimentally.

Although Boroditsky's essay could be construed as implying that most of the research has been done in her laboratory, in fact it has been undertaken rather more widely. However, we won't attempt to survey the other work right now. Let's just recap some of the research findings she discusses.

One interesting group of studies is anthropological in origin, like the original investigations of Sapir and Whorf. It involves how the languages of certain Australian aborigines, including but not limited to a group known as the Kuuk Thaayorre, describe 2-dimensional space. In English, and indeed in most languages of which English speakers have ever heard, positions in 2-dimensional space, in which the observer is situated, are usually described relative to the observer: left vs. right, in front of vs. behind. But for the aborigines, 2-dimensional space in which they are located is described in terms of absolute directions: north, south, east, west. Such a system has obvious advantages for navigation in possibly unfamiliar territory, by forcing the observer to remain oriented to fixed directions. It's also natural for people who spend a lot of time outdoors. This anthropological fact has been known for some time.

Many languages can apply spatial concepts to non-spatial information as well, particularly in the special-case of 1-dimensional data of many types. Examples include size, weight, age, time ("earlier" vs. "later"), moral values ("better" vs. "worse"), kinship ("near" vs. "far"), musical pitch ("high" vs. "low"). (It's now understood, of course, that pitch can be quantified as vibrational frequency, but this is a modern development.)

Each of these examples either involves things that can be quantified using numbers (size, weight, age), or if that's not possible there are terms specialized for the particular concept. Quantifiable concepts generally also have their own special terms too, which indicate magnitude in a vaguer way, when numeric values aren't convenient ("big" or "small", "heavy" or "light", "old" or "young").

In the case of quantifiable concepts it's not unusual to think of attribute values spatially laid out on a line from smaller to bigger (though the actual direction in space may vary – left to right or right to left, for example). Some concepts that aren't obviously quantifiable also customarily involve spatial metaphors (kinship, pitch).

Other concepts more often are described with non-spatial terms, but sometimes admit spatial metaphors. For instance, a particular time may be "near" or "distant", like kinship. Moral values may be "higher" or "lower", like pitch.

Obviously, languages other than English may customarily use different terms and metaphors to describe the same concepts. Every language seems to have its own way of conceptualizing and describing certain things, even with quantifiable concepts. Consider time, for example. Sometimes it's represented in non-spatial terms ("earlier" vs. "later"), but spatial metaphors are also common ("before" vs. "after"). When thinking spatially of time, English speakers tend to think of it in a horizontal line, perpendicular to the observer's line of sight, from earlier to later (and usually left to right). Occasionally time is described, like kinship, in a line that runs outward from the observer. However, Mandarin arranges time in a vertical direction – the way English arranges musical pitch.

(There are obviously even more complexities in all this if similar concepts customarily used in differing languages aren't quite congruent or coextensive to begin with. For instance, the concept "moral values" is one thing if such values are customarily believed in one culture to be supernaturally ordained, but something rather different if they are thought to be products of a rational ethics.)

In mathematics there is a uniform way of dealing with such 1-dimensional concepts. This is especially true when the concepts are quantifiable, but it also true even when there is only a greater-than-less-than relationship between specific attributes of different individuals. This kind of relationship of attribute values is called a linear ordering. However, most people, and most languages, don't express things in abstract mathematical terms. And so the actual language used for different types of linearly orderable attribute values can vary dramatically from one language to another.

With all these ways of using metaphors and terminology, which vary from language to language, for describing concepts, one can't help but wonder whether the choice of terminology or metaphor in a particular language affects how a speaker of the language thinks about a concept. For instance, does use of a spatial metaphor for moral values ("higher" or "lower") predispose a speaker to think differently about the concept than a different metaphor ("conservative" or "liberal", say)? If we are comparing different languages, do the different customary metaphors employed lead to observable differences between cultures where one or the other language predominates?

So the interesting general scientific question that arises from this situation is whether the peculiarities of how a particular language describes certain types of attributes have an effect on how the speakers of the language think about the attributes. More specifically, is it possible to set up experiments that demonstrate consistently different behaviors by speakers of different languages, where the behaviors make sense in terms of how each language typically represents the attributes?

When, as is quite common, a single language offers choices of metaphors or terminology for describing a given concept, it should be easy to set up experiments to detect different ways people think about a concept (as determined by observable behavior) according to selections of metaphor or terminology presented to an experimental subject. Or better yet, can we measure how much or how likely use of a specific metaphor affects specific behavior with respect to a given concept under given conditions?

This kind of experiment, that uses only speakers of a single language, can separate out effects due to language (as expressed in metaphor or terminology) from effects due to underlying culture, as long as experimental subjects are drawn from the same culture or classified by culture (or specific demographic or ethnic groups, for example). This is a way to deal with the questions that always arise about whether it's the language or the culture in which the language is spoken that accounts for observed differences. A similar option, which Boroditsky mentions, is to deliberately train experimental subjects to use unfamiliar metaphors or terminology drawn from languages other than the subject's native language.

Boroditsky cites a few examples of experiments that have been performed to study such questions. In addition to considering languages that use different spatial metaphors (either 1- or 2-dimentsional), she mentions experiments involving other types of language differences. One example is whether and how "gender" is encoded in the grammar of a language. English is a little unusual in not having much grammatical role for gender (except for pronouns). In Russian, however, most nouns have one of three genders (masculine, feminine, neuter). In a Russian sentence, adjectives, pronouns, and even verbs that refer to a noun must agree in gender.

As Boroditsky notes, "some Australian Aboriginal languages have up to sixteen genders, including classes of hunting weapons, canines, things that are shiny." Although English and other Indo-european languages seem to rely on sex (i. e. genitals – same linguistic root as "gender") as the metaphor for gender, in other languages gender is simply about whatever the language, or the underlying culture, considers to be the most important categories for partitioning the world of discourse. Obviously, this can lead to huge differences in how people who use different languages think about the world.

Or consider the way languages differ in how they divide up a space of perceptual qualia – color in particular. Russian, for instance, recognizes two different types of blue (varying in the brightness dimension), using different words. This can lead to observable differences in behavior between Russian and English speakers. (Of course, English also recognizes multiple types of blue, such as azure and blue-green. It may simply use hyphenated and compound words to denote many of the different types. There may be thousands of English terms. What's distinctive about Russian is that it doesn't have a single word that is applicable to something that's normally just "blue" in English.)

It would be very interesting to study linguistic effects with respect to other types of qualia, such as taste. Taste is especially interesting, since there are physiological reasons that, cross-culturally, five different "flavors" are commonly recognized: "sweet", "salty", "sour", "bitter", and "umami". The result is a 5-dimensional perceptual space, instead of the 1-dimensional space of loudness or hue. For that matter, color space is actually 3-dimensional (hue, saturation, brightness), and sound has various dimensions too (loudness, pitch, timbre, etc.)

All this raises many interesting questions. How much do languages vary in the way they conceptualize perceptual spaces? Even if spatial dimensions are the same between two languages, are the spatial axes oriented differently? And what effects do such differences have on how people think about the perceptual spaces?

Interestingly, even in the case of color, the strength of a linguistic effect on perception of hue (e. g. 1 vs. 2 types of blue) seems to depend on how much the experiment calls for cognitive processing in the left vs. the right brain hemisphere, presumably because of the special role of the left hemisphere in language processing.

And then, supposing some correlation exists between how languages represent certain attributes and how people behave in thinking about the attributes, how can it be decided whether the language has affected the thinking, as opposed to both language and thought being affected by cultural history and circumstances (such as a lifestyle that places high importance in being oriented to directions of the compass). Boroditsky suggests experiments that can be done, such as deliberately teaching people different ways of describing things, to find out whether and how this affects thought and behavior.

But let's begin to wrap this up by returning briefly to Boroditsky's observations of the Kuuk Thaayorre. There was a specific reason she wanted to study these people. As noted, it was known that they tended to think of (2-dimensional) spatial information using coordinates independent of the observer. That's also true in thinking about 1-dimensional data, which speakers of English (and most other language) think of as left vs. right, relative to the observer.

Boroditsky wanted to know how the Kuuk Thaayorre conceptualized and described other 1-dimensional linear orderings, such as time, where spatial metaphors are less likely to be used in other languages. The answer is that the Kuuk Thaayorre continued to use the same absolute coordinate system for such things. For example, given pictures illustrating temporal progressions, they would tend to arrange them in a line in the east-west direction. So not only did they stick to absolute coordinates, but they chose a direction that just happens to be the same as the Sun's motion through the sky – as opposed to north-south, say. Of course, that might be due to dealing with temporal information.

One wonders whether they would do the same with other linearly ordered data, such as taste of food (from "unpleasant" to "delicious"). One also wonders what the outcome of such experiments would be if they were done with Kuuk Thaayorre people indoors, under conditions where they would be unaware of actual compass directions.

Interestingly, speakers of English and other languages that are written in a left-right direction, tend to arrange pictures illustrating temporal progression in the same left-right direction, while speakers of languages written from right to left tend to use this right-left ordering for 1-dimensional data. Right there you have an apparent effect of language on thought patterns and behavior.

Concluding thoughts

This is a vast subject. It's not at all easy to summarize even the discussion presented here. So I won't try. I'll just add some general remarks.

It has generally been assumed that if there is any causal relationship between language and thought it should be in the direction of language affecting thought instead of vice versa. This is probably because language is assumed to have arisen without conscious design, and because it's difficult to imagine what relatively complex thought would be like if it came before language. We assume that non-human animals, which lack language, can't have complex thoughts. But we know almost nothing about the origins of human language, at least tens of thousands of years ago, or what human thinking might have been like at the time. Our assumptions could be wrong. Language and complex thought probably co-evolved to some extent that we can now only guess about.

For another thing, it should be obvious that the effect of language doesn't have to be all or nothing. The Whorfian Hypothesis isn't necessarily generally true or generally false. Instead, what needs to be investigated are tendencies and correlations under many different special conditions, such as the kind of cognitive activity one suspects might be affected. One should look for the strength (i. e. probability) of an effect, and its pervasiveness (i. e. range of circumstances in which it can be observed).

Another important consideration is that language has a variety of parts, with vocabulary and grammar being the major divisions. The vocabulary and grammar of a language probably differ a lot in whatever way they affect thinking.

As far as vocabulary is concerned, if a language lacks a word for a specific concept, it's considerably more difficult to think about the concept, though generally not impossible. Without a word for a concept, it's harder to keep it in mind in order to examine it logically in order to understand it, or to use it for classifying or organizing things. For example, a study of an Amazonian tribe, the Piraha, who don't have words for numbers, suggests that these people have difficulty with numerical concepts in tasks where memory is involved, even though they presumably can recognize differences in size of small collections of things. (See below for more about this study.)

Likewise, suppose we didn't have words for many types of mammals, how easily could we distinguish between a fox and a coyote, say? Whether we regard two things as the "same" or "different" depends a lot on whether we have separate, common words for the two things. (For example: different shades of the same color.) Even if we could visually perceive differences between the species, would we remember the differences long enough to keep track of other ways the species differed?

So languages with sparse vocabularies make many kinds of thinking difficult. In language without words for abstract concepts like "liberty", "freedom", "justice", etc. it would be difficult to develop much of a political philosophy. Indeed, the introduction of such terms is often the starting point for new directions in philosophy. All this argues for a significant effect of language on thought, mediated by the language's vocabulary.

But vocabulary is a rather different aspect of language from grammar, and it is the grammar of a language that is often the focus of questions about how language affects thought. For instance, there are all the questions about the role of grammatical gender. Other important grammatical issues have to do with verbs – the way in which they involve time ("tense"), attitude towards the action ("mood"), whether action is ongoing or completed ("aspect"), issues of effect of an action ("transitivity") and so forth. A language can potentially pack quite a variety of disparate kinds of information in its verbs. Each of these aspects of grammar may affect thinking in different ways and different degrees. Research should be looking for whether certain aspects tend to be more influential than others.

Another interesting difference between vocabulary and grammar is that the former probably changes more quickly than the latter. Indeed, a language's grammar tends to change pretty slowly, and in small increments, if at all, over hundreds of years. But vocabulary can change in a matter of decades, or less. Think of the difference in English vocabulary between Shakespeare's time and ours. (With Shakespeare himself responsible for quite a few innovations.) Yet the grammar of Shakespearean English is hardly different from that of contemporary English.

What this may mean is that the grammar of a language has a more profound effect than vocabulary on thinking because of its relative constancy. Consequently, perhaps, speakers of the language can hardly imagine that distinctions imposed by grammar might admit any possible alternative kinds of distinctions. Just as speakers of English have a difficult time imagining any relevance of gender to non-living things.

Lastly (for now), I should point out the relevance of this discussion to the even more general topic of "social construction of reality", as briefly touched on here.

In that regard, Edward Sapir wrote: "No two languages are ever sufficiently similar to be considered as representing the same social reality."

A few recent relevant research reports

Language Without Numbers: Amazonian Tribe Has No Word To Express 'One,' Other Numbers (7/15/08)
An Amazonian tribe, the Piraha, with only 300 speakers of its language, apparently has no words for any natural number, even "one", though it has terms for comparing quantities ("some", "more"). Consequently the size of a very small collection (1 to 4 things) would be described with a word meaning "few", while larger collections would be "many".

Aboriginal Kids Can Count Without Numbers (8/18/08)
In contrast to the preceding report, a study of children in two Australian aboriginal communities, whose language does not contain words for numbers, showed that the children were able to copy and perform number-related tasks.

Pre-verbal Number Sense Common To Monkeys, Babies, College Kids (2/15/09)
As in a number of other studies, this research shows that human infants, as well as macaque monkeys, show an awareness of the different size of very small sets (2 or 3 objects), even though they do not have language. In fact, even dogs have a similar awareness, using similar testing protocols. (See here.) So certainly the Piraha also have such awareness. But as is pointed out in the Piraha study, lack of words for numbers seems to significantly affect the ability to perform tasks where memory is involved.

Scientists show that language shapes perception (2/26/09)
Modern Greek, like Russian, has different words for light and dark blue, unlike English. Greek speakers automatically use different words to describe the color of the sky or the color of the ink of a (dark) blue pen. Using a measuring technique called "event related brain potentials", differences in brain activity caused by seeing different shades of blue can be detected before the appropriate color word enters consciousness. However, this doesn't necessarily mean that the brains of Greek speakers and English speakers (say) are genetically different – only, perhaps, that the cultural habit of sharply distinguishing two kinds of blue has been learned in non-verbal, as well as verbal, parts of the brain.

Expressing comparisons is possible even without language, researchers find (6/30/09)
Deaf children who had not learned a spoken language were compared with hearing children who had learned some language. Deaf children are able to use gestures to indicate a recognition that (for example) a house cat is different from a tiger. However, "as the children grew older, the comparisons diverged — deaf children's comparisons remained broader in nature, while hearing children's comparisons became more complex and focused, such as saying that the hair was brown like a brown crayon, after hearing children started using the word 'like'."

Update, 8/24/09: Here's a relevant new article I haven't had a chance to evaluate yet: Does Language Shape What We Think?

Update, 9/4/09: And here's an interesting quote from Steven Pinker (via Amira):
Human beings do not live in the objective world alone, nor alone in the world of social activity as ordinarily understood, but are very much at the mercy of the particular language which has become the medium of expression for their society. It is quite an illusion to imagine that one adjusts to reality essentially without the use of language and that language is merely an incidental means of solving specific problems of communication or reflection.

The fact of the matter is that the ‘real world’ is to a large extent unconsciously built up on the language habits of the group … We see and hear and otherwise experience very largely as we do because the language habits of our community predispose certain choices of interpretation.

Tags: , , social construction of reality

NASA's Spitzer Images Out-of-this-World Galaxy

Wednesday, August 5, 2009

NASA's Spitzer Images Out-of-this-World Galaxy (7/23/09)
NASA's Spitzer Space Telescope has imaged a wild creature of the dark — a coiled galaxy with an eye-like object at its center.

The galaxy, called NGC 1097, is located 50 million light-years away. It is spiral-shaped like our Milky Way, with long, spindly arms of stars. The "eye" at the center of the galaxy is actually a monstrous black hole surrounded by a ring of stars. In this color-coded infrared view from Spitzer, the area around the invisible black hole is blue and the ring of stars, white.

The black hole is huge, about 100 million times the mass of our sun, and is feeding off gas and dust along with the occasional unlucky star. Our Milky Way's central black hole is tame by comparison, with a mass of a few million suns.

NGC 1097 – click for 1000×1000 image

More: here, here, here

NASA's Spitzer Sees the Cosmos Through 'Warm' Infrared Eyes

NASA's Spitzer Sees the Cosmos Through 'Warm' Infrared Eyes (8/5/09)
NASA's Spitzer Space Telescope is starting a second career and taking its first shots of the cosmos since warming up.

The infrared telescope ran out of coolant May 15, 2009, more than five-and-a-half-years after launch. It has since warmed to a still-frosty 30 degrees Kelvin (about minus 406 degrees Fahrenheit).

New images taken with two of Spitzer's infrared detector channels — two that work at the new, warmer temperature — demonstrate the observatory remains a powerful tool for probing the dusty universe. The images show a bustling star-forming region, the remains of a star similar to the sun, and a swirling galaxy lined with stars. ...

The first of three images shows a cloud bursting with stars in the Cygnus region of our Milky Way galaxy. Spitzer's infrared eyes peer through and see dust, revealing young stars tucked in dusty nests.

Cygnus region – click for 750×663 image

Disney Elevates Heterosexuality To Powerful, Magical Heights

Tuesday, August 4, 2009

It's common to think of "the media" as providing a window on the "real world" that's imaginative and metaphorical – ostensibly to make it more "entertaining" – yet nevertheless essentially accurate.

At some level people also know and, to an extent, understand and even approve that mass media are distinctly slanted to celebrating and inculcating the majority ideology and values of the society in which they are embedded.

What doesn't seem to be generally understood, though, is how distorted the resulting picture of the "real world" can be, in order to reinforce the fortuitous ideology and values prevailing in any given society.

Here's research demonstrating how extreme the distortion can become. And the focus on Disney is so appropriate. It is so exquisitely fitting that a place called "Fantasyland" is found at the heart of Disney's theme parks Disneyworld/Disneyland. It's a metaphor for what is to be found at the heart of "real world" societies.

Disney Elevates Heterosexuality To Powerful, Magical Heights (6/22/09)
Martin and Kazyak analyzed all G-rated movies released, or rereleased, between 1990 and 2005 that grossed more than $100 million in the United States (see Supplemental Materials). Three trained research assistants extracted story lines, images, scenes, songs and dialogue that addressed anything about sexuality, including depictions of bodies, kissing, jokes, romance, weddings, dating, love, where babies come from, and pregnancy. The text describing this material was inductively coded using a qualitative software program.

The analysis found the films "depict a rich and pervasive heterosexual landscape," despite the assumption that children's media are free of sexual content. The movies repeatedly mark relationships between opposite sex lead characters as special and magical.

Research article abstract:

Hetero-Romantic Love and Heterosexiness in Children's G-Rated Films
In this article, the authors examine accounts of heterosexuality in media for children. The authors analyze all the G-rated films grossing $100 million dollars or more between 1990 and 2005 and find two main accounts of heterosexuality. First, heterosexuality is constructed through hetero-romantic love relationships as exceptional, powerful, magical, and transformative. Second, heterosexuality outside of relationships is constructed through portrayals of men gazing desirously at women's bodies. Both of these findings have implications for our understanding of heteronormativity. The first is seemingly at odds with theories that claim that heterosexuality's mundane, assumed, everyday ordinariness lends heteronormativity its power. In fact, the authors suggest heterosexual exceptionalism may extend the pervasiveness of heterosexuality and serve as a means of inviting investment in it. The second offers ways to begin to think about how heteronormativity is gendered and racialized.

Tags: , , social conditioning, social construction of reality

Brain simulation

Monday, August 3, 2009

Recently there was a considerable splash (some would unkindly call it hype) about an ongoing simulation project that might produce an "artificial human brain" within 10 years from now:

Artificial brain '10 years away' (7/22/09)
A detailed, functional artificial human brain can be built within the next 10 years, a leading scientist has claimed.

Henry Markram, director of the Blue Brain Project, has already simulated elements of a rat brain.

He told the TED Global conference in Oxford that a synthetic human brain would be of particular use finding treatments for mental illnesses.

Around two billion people are thought to suffer some kind of brain impairment, he said.

"It is not impossible to build a human brain and we can do it in 10 years," he said.

The project isn't brand new. It was formally initiated in June 2005 by EPFL, the École Polytechnique Fédérale de Lausanne (in Switzerland), in cooperation with IBM. This Blue Brain project has been directed since the beginning by Henry Markram of EPFL. The project's name is derived from its use of an IBM Blue Gene computer for performing the simulations.

An initial goal of the project was completed after just 1.5 years, in 2006 – the simulation of a single rat cortical column. While that's a noteworthy accomplishment, keep in mind that a human cortical column contains 6 times as many neurons (60,000) as does the rat equivalent.

In addition, although the architecture of each column is roughly similar to that of any other, the total number of columns in a human cerebral cortex is estimated at about 2 million. (The cerebral cortex is the outermost, and evolutionarily most recent, part of the human brain, in which the most sophisticated processing occurs.) The project is facing a rather daunting amount of simulation that needs to be performed.

The present flurry of excitement over the project stems from a presentation by Markram at the recent TEDGlobal 2009 conference.

While a video of Markram's talk doesn't seem to be available online yet, you can find some blogged notes here: Henry Markram at TEDGlobal 2009: Running notes from Session 5.

Here are some additional references on the talk and the project in general:

Note that the caption on the last video in this list observes that a complete simulation may require a computer 20,000 times as powerful as any currently existing computer. (At current rates of progress, we would see a computer "only" 1000 times as powerful in 10 years.) Such a computer would also need a memory capacity 500 times the size of the Internet. Anyone else sense a discrepancy with claims made more recently?

Later additions:

Competition in the wings?

Before passing on to a skeptical take on the feasibility of what the Blue Brain project proposes to do, it's rather interesting that there may be competition in this race – and in part from no less than another portion of IBM:

Cognitive Computing Project Aims to Reverse-Engineer the Mind (2/6/09)
"The plan is to engineer the mind by reverse-engineering the brain," says Dharmendra Modha, manager of the cognitive computing project at IBM Almaden Research Center.

In what could be one of the most ambitious computing projects ever, neuroscientists, computer engineers and psychologists are coming together in a bid to create an entirely new computing architecture that can simulate the brain’s abilities for perception, interaction and cognition. All that, while being small enough to fit into a lunch box and consuming extremely small amounts of power.

The 39-year old Modha, a Mumbai, India-born computer science engineer, has helped assemble a coalition of the country’s best researchers in a collaborative project that includes five universities, including Stanford, Cornell and Columbia, in addition to IBM.

The researchers’ goal is first to simulate a human brain on a supercomputer. Then they plan to use new nano-materials to create logic gates and transistor-based equivalents of neurons and synapses, in order to build a hardware-based, brain-like system. It’s the first attempt of its kind.

Sort of makes one wonder what's going on here, no? I don't have any further information on this project, except some details on Dr. Modha, and further references contained therein (especially the first item):

And now for the skeptical view

You knew it was coming, right?

Here's video of a debate on this topic (in general, not either IBM simulation project in particular) between John Horgan (the skeptic) and Ray Kurzweil (in rebuttal).

Ray Kurzweil and John Horgan debate whether a singularity is near or far

And here's an article by Horgan with the details of his argument:

The Consciousness Conundrum

I don't always agree with Horgan, but his case on this topic seems a little more persuasive at this point.

In support of Horgan's point of view, I could mention an article from March 2009, about the work of the Allen Institute for Brain Science. It's written by Jonah Lehrer, who earlier wrote on the Blue Brain project in one of the references cited above:

Scientists Map the Brain, Gene by Gene
One unexpected—even disheartening—aspect of the Allen Institute's effort is that although its scientists have barely begun their work, early data sets have already demonstrated that the flesh in our head is far more complicated than anyone previously imagined. ...

"The brain is just details on top of details on top of details," Hawrylycz says. "You sometimes find yourself asking questions that don't have answers, like 'Do we really need so many different combinatorial patterns of genes?' ...."

"The problem with this data," one researcher told me, "is that it's like grinding up the paint on a Monet canvas and then thinking you understand the painting." The scientists are stuck in a paradox: When they zoom in and map the brain at a cellular level, they struggle to make sense of what they see. But when they zoom out, they lose the necessary resolution. "We're still trying to find that sweet spot," Jones says. "What's the most useful way to describe the details of the brain? That's what we need to figure out." ...

Although the human atlas is years from completion, a theme is beginning to emerge: Every brain is profoundly unique, a landscape of cells that has never existed before and never will again. The same gene that will be highly expressed in some subjects will be completely absent in others.

Additional skeptical views:

I think I'll need a bit more time to digest the information here...

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