var _gaq = _gaq || []; _gaq.push(['_setAccount', 'UA-35679719-1']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Iâm Kati and I went to school for molecular biology, but I love all kinds of science. The Science Age is for exploring and understanding all the interesting things going on in scientific research and how they fit in to our lives. Contact me at The Science Age at gmail dot com (no spaces) or
A few years ago, Harvard's BioVisions group put out some really amazing videos, including The Inner Life of the Cell embedded here. Unfortunately, for all their intricate and true-to-life visual detail, there isn't narration to describe the things you're seeing. I'm going to work through this video and their others, but for now just enjoy! (My favorite is the motor protein featured starting at 3:40.)
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Last month, the Washington Post moderated a discussion about the broad themes and implications of astrobiology with NASA and the Library of Congress's specialized chairs (video here). They bring up some very interesting scientific ideas, and since we don't currently know of any life outside of Earth we'll just have to wait and see.
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For example, it doesn't actually seem that hard to begin life from a biochemical standpoint. The particulars of how our branch of life began are difficult to ascertain and we haven't synthesized any totally artificial species, so that's not to say it's easy, but given the ubiquity of certain elements and exponential ways or ordering them, as well as the relatively young age of Earth, it's not theoretically unlikely. Of course there may be limits we haven't considered yet, and some scientists do put stricter boundaries on the possible biochemical bases of life, but it's a reasonable and inspiring idea.
On the other hand, evolution isn't directional, it simply favors species that can stay alive. Since staying alive doesn't require complex intelligence, it's completely possible (even likely, if you consider humans to be the only intelligent species on Earth) that alien life would not have it. Moreover, even if an alien species was intelligent, it could be a very different kind of intelligence. Different environmental conditions and evolutionary pressures could emphasize completely different processes - for instance the hypothetical presented by a SETI researcher in this article, where smell, rather than sight or sound, is the primary sense, precluding the development of abstract mathematics because they are not particularly apparent or useful.
Of course, taking the view that extraterrestrial life could develop in such an immense range of circumstances isn't really helpful in our search for it. That's why NASA's astrobiology-focused exoplanet research is looking for somewhat Earth-like conditions, at least for now.
In an effort to show just how empty most of the solar system is, designer Josh Worth has designed a scrolling webpage that shows the sun, planets, and moons at relatively accurate sizes and distances. Our moon is designated as one pixel big, and the rest of the solar system is scaled to fit. It's certainly not the first time it's been done, but it's simple and well-done.
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As noted in the project's description, looking at the solar system in this way is somewhat of an exercise in tedium. Planets are massively far apart, on a scale that's hard to really visualize. The act of scrolling across so much empty space helps to demonstrate that, as does the corollary that it's impossible to show the solar system at both accurate sizes and distances on a regular computer screen. If you shrank everything down to fit within 1280 pixels, nothing, not even the sun, would be big enough to fill one pixel. (And that's just calculating the distance from the sun to Neptune; express your love for Pluto all you want, it's not a planet.)Â It really helps put into perspective why things like interplanetary missions, let alone the Voyagers, take years or decades to complete. With that in mind, I'd really recommend scrolling rather than clicking through the illustration (there are informative and funny comments in space along the way to keep you occupied).
If you're feeling ambitious, you can try to scale up the visualization to interstellar space - at its closest edge our solar system ends around four times further out than Neptune, and Proxima Centauri, the closest star to our sun, is over 9000 times further away than Neptune. This is why you don't want to diagram stars on the same scale as planets; you'd be scrolling through empty space 9000 times again as long as you just did in Josh Worth's illustration. If instead you scaled our entire solar system to one pixel (even though the vast majority of that pixel would actually be empty space), Proxima Centauri would be seven computer screens away.
A recent study published in PNAS (and summarized in ScienceShot) seems to have figured out why there are no fish in the deepest parts of the oceans. Essentially, they propose that itâs due to a limit imposed on fish biochemistry as result of an evolutionary adaptation not developed with those depths in mind. (It's also a succinct counterpoint to the idea of evolutionary directionality. Ideally, there would be a fish species that could live in the deepest parts of the ocean, but it appears that real fish are limited by a random quirk of a molecule that evolved at shallower depths, without these extreme depths in mind.)
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The deeper under water you go (as with any fluid on earth) the more pressure that water exerts on you. As the paper notes, descending 100 meters (the length of a football field) increases the pressure by 10 atm (for reference, 1 atm is the about the pressure we experience here on the surface of the earth). Seeing as the deepest parts of the ocean are around 11,000 meters deep, thatâs an enormous amount of pressure. Living things are sensitive to pressure on a number of structural scales, from organs (which can rupture at excessively high or low pressures) to individual cells (likewise, killing them and impairing tissue functions) to proteins (which can deform, rendering them biologically useless).
To deal with issues of pressure on protein deformation, fish have evolved a molecule, called TMAO (trimethylamine N-oxide) which stabilizes proteins within their cells. TMAO counteracts the effects of water pushing into proteins at high water pressures, allowing the proteins, and therefore the fish, to survive in deep water.Â
At the same time, fish cells (like all vertebrate cells) are sensitive to how many particles are within them relative to how much water. Those particles (like proteins and nutrients) are critical for a cellâs life, but so is the amount of water (to maintain its structure and biochemical processes). The ratio of the two, the concentration inside a cell, must be maintained on a very particular range or the cell will die. Vertebrates depend on having a concentration within their cells that is a certain ratio lower than the concentration outside their cells. For fish, that outside is the ocean.
Based on some earlier research, the researchers had reason to believe that the amount of TMAO necessary to keep proteins functional is proportional to the amount of pressure: the greater the pressure, the greater the amount of TMAO must be present in cells. Fish, therefore, have two competing necessities. On one hand, they need TMAO at increasing concentrations to survive at lower depths. On the other, they need their overall cellular concentrations to be lower than that of seawater. The researchers of the PNAS paper calculated the theoretical limit imposed by this balance: at 8,200 meters below the surface of the ocean, a fish would need so much TMAO that itâs cellular concentration would match that of the surrounding water. So, fish should not be able to survive below 8,200 meters, since having the same or a higher cellular concentration would kill it.
To test this idea, the researchers measured the concentration of TMAO in related fish species living at different depths, from 900 to 7,000 meters. They found that there really was a proportional relationship between the depth and the concentration of TMAO in the fish. They also found that those concentrations lined up with their predictions, supporting the idea that 8,200 meters is an approximate biochemical limit. These findings, paired with the fact that no living fish has ever been found below 8,370 meters (with that one record-holder standing far ahead of the rest of the pack, which have been above 7,700 meters), support the proposal of a depth limit for fish based on a biochemical balance between TMAO and ocean salinity.
The authors acknowledge that their evidence doesnât prove this to be the case. Just because no fish have been found beyond that limit so far doesnât mean there arenât any, or there are other factors related to depth (such as nutrient availablity) that could be the real cause of the limit. Alternately, the cause could be related to TMAO but not ocean salinity: it could simply be that the concentrations of TMAO required for greater depths are toxic to the fish. Or, everything proposed in this paper might be correct, but there may be deeper-living fish that have evolved an independent mechanism to resolve its pressure and concentration problems. Those gaps being pointed out, it's a fascinating finding in a emerging area of research.Â
[Image shows two snailfish, the deepwater species sampled in the study, and a bystander brittle star from the ScienceShot article.]
Evolution is so widely known that it's constantly referenced, even outside biology. It turns up as an explanation for everything from bird plumage to an artist's career. Evolution is a critical concept in biology and a useful metaphor for most processes tangentially related to life. The idea is fairly simple. In order to survive, living things have to either continue living (which only gets you so far) or reproduce. Since no life is immortal, survival of related things is the important thing, and reproduction is the long-term key to group survival. Therefore, whatever groups reproduce and allow those progeny to live, will survive. Changes in living things, like DNA mutations, can lead to a better (or worse) chance of survival. Whatever ends up surviving, still exists; anything that can't keep up, dies out.
However, people (especially when using it as a metaphor) tend to ascribe evolution additional principles, like directionality. Directionality is the idea that evolution is moving towards something, and it's completely out of place in understanding evolution.
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The idea of directionality seems to be a by-product of the fact that humans defined evolution. We see ourselves as bigger, more complex, more social, and more intelligent than the other things living today and assume that this is better. We assume that evolution has built up to us, the ideal living things. That is just not true. It may be the case that we are bigger or more intelligent (although this is evaluated by our own tests, so it's tricky to know what we're really measuring), but there are obviously smaller and less intelligent things still surviving. There is no reason, from the perspective of evolution, that one subset of currently living things would be ideal and none of the myriad of others, or that one set of traits would be more ideal than the others.
A recent article in Nautilus covers a lot of this issue in more detail (although it implies a lot more contemporary sympathy for directionality than I've encountered in the scientific community). The popular support of directionality certainly does originate in the (antiquated) scientific acceptance of it though. Fortunately, evolutionary biologists have started to correct the directionality bias, visibly evident in the revised, non-hierarchical "tree" of life diagrams.
Moreover, directionality implies intentionality. If evolution is working towards something, it has to know where it's going. This blatantly contradicts the mechanisms of evolution, which are random alterations played out in survival and reproduction. Evolution is a convenient name for a natural process (similar, in that way, to gravity), it's not a conscious entity with control over living things.
The idea of directionality in evolution, in addition to just being wrong, leads to insidious misunderstandings, such as the popular idea that humans have stopped evolving or that other living things are less evolved than us. If you look at the actual concept of evolution, this idea is absurd. Nothing living can ever stop evolving. The rate of mutations can change, as can the particular selective pressures, but evolution itself never stops. Either a group is alive and evolving, or extinct.
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Hi everyone, I'm still in the throes of applications, but here are a couple interesting articles about the confusing nature of time! Time in physics can be profoundly different than time in our normal, everyday lives, and some of the theoretical possibilities are both fascinating and very hard to wrap your head around.
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Scientific American has an interesting article describing the idea of "rainbow gravity."Â Essentially, rainbow gravity says that, different wavelengths of light react differently to the same gravitational influence. The technical aspects are beyond me, but according to Scientific American this idea could account for the separate worlds of general relativity (which as we understand it today operates on large scales but not tiny ones) and quantum mechanics (which covers the tiny scales but currently does not work at large ones). Additionally, it has interesting implications for the origin of the universe. Whereas most models start from the familiar big bang, rainbow theory does not. There is currently no evidence to support rainbow gravity over other ideas, but it is a possibility, and experiments have been proposed that are beginning to be technologically feasible which could bolster or detract from it.
Nautilus has a great article following the work of John Wheeler, who (among many other things) proposed an alternate way of unifying general relativity and quantum mechanics. Wheeler is famous for conducting the delayed choice extension of the double slit experiment. Within the rules of quantum mechanics, the behavior of light counterintuitively depends on whether it is being observed or not. The double slit experiment shows that a unit of light can either take one of the possible paths available to it (like a person taking one route to the grocery store, which makes intuitive sense) or all possible paths at once (like one person simultaneously walking every possible way to the store, which is very weird) depending on whether you monitor which path it takes. Wheeler took this a step further by realizing that, in quantum mechanics, it doesn't matter when you make this observation. The delayed choice experiment shows that you can actually causally determine how the light behaves (taking one path or all of them) by choosing to observe the path or not after the light has already started traveling. This apparent reversal of cause and effect is mind-boggling, but can be understood and has been proven to happen in quantum mechanics. Wheeler proposed that the entire universe might be a quantum system, and that our act of observing the big bang could actually have caused it. A new version of this idea is supported by Steven Hawking and Thomas Hertog in "top-down cosmology," which they aim to test using measurements of the Cosmic Microwave Background.
(Image is an illustration of what happens when you conduct the double slit experiment without an observer. From the science communication blog of Australian National University)
I'm busy with grad school applications right now and won't be posting regularly until the spring, but here's an update.
Scientific American has an interesting (if a bit alarmist) article on the burgeoning disagreement between 23andMe and the FDAÂ (as I brought up earlier, 23andMe is in an interesting ethical spot as a commercial biotech company). 23andMe has started pushing the healthcare benefits of knowing your own genome. While it's certainly true that many health problems have genetic factors, many have not been adequately studied at this point, including some of the claims 23andMe is using in its advertising. The FDA is in charge of regulating products or services that are used to identify diseases or risk factors, and they're saying that since 23andMe has not proven their claims or methodology, they need to stop. NPR also has a piece on the warning, where you can listen to clips of the disputed ads.
Hi, Iâm back! At the perfect time to update on my last topic, removing the wrecked Concordia cruise ship from a rock ledge off the coast of Italy. Since I last wrote, salvagers have been working constantly to enact their plan to rotate the ship upright, float it with external ballasts, and tow it away. As of today, theyâve succeeded in the first step.
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While the stages to come will pose their own challenges, the ships rotation was one of the greatest uncertainties. Salvage planners had to balance the need to learn as much as possible about the structural state of the ship with the fact that every hour it spends in its current state furthers its decay. In an engineering operation of this size, it simply isnât possible to know all the variables ahead of time; planners were making their safest, best, educated guess. And it wasnât without its risks. Rotating the ship caused even more strain on its structure, in places and directions it wasnât designed to withstand. Itâs already been under a huge amount of stress lying on its side for the past year and a half. If the ship wasnât quite sound enough in any one place during the rotation it could break apart, littering the coral reef with debris and ruining any chance of a complete salvage. On the other hand, it was possible for the supports salvagers put in place to facilitate the rotation to break under the strain, rolling the whole ship down the rocky hill itâs been precariously resting on.
The good news is that salvagers have dodged the first problem. The Concordia successfully rotated (over the course of almost a full day) without any extra damage to the hull, allowing it to come fully upright. Now itâs resting on the underwater platform, awaiting installation of additional ballast chambers that will be used to float the remains of the ship as high above the water as possible, preparing it for the tow away. Not that these steps will be much easier. As this Scientific American piece notes, the sponsons for the damaged side need to be individually formed and attached, and the process isn't slated to be done until the spring. And then, of course, final adjustments have to be made for the refloating and towing. I'll continue posting updates as the operation progresses!
You can see a time-lapse video of the rotation maneuvers at Time.Â
[photo by Andreas Solaro/Agence France-Presse - Getty Images, via the New York Times article]
Last year, the Concordia cruise ship hit a small Italian island in the middle of a reef system, killing & injuring passengers and wrecking the ship. Now, salvagers are attempting to remove the ship from the seabed and minimize the damage to the reef ecosystem.
As this thorough article in Nature describes, this is really an intricate and unprecedented process. (The Nature article requires a subscription for access, but thereâs a short preview on Scientific American) Traditionally, wrecked ships are purposely sunk to get them off the surface, and thatâs that. While that tactic solves the immediate problem, the ship and the things it carries (like food and oil) arenât very good for the environment theyâre then left in. Thatâs especially true for coral reefs, which are notoriously diverse but delicate ecosystems. The Italian government is requiring a thoroughly-planned attempt to right the ship and tow it away back to shore, hoping to limit any damage to the underwater environment.
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The process is massive in scale but relatively easy to understand. Salvagers have already wrapped the ship in chains attached to anchoring stanchions to hold it in place. No one wants it to shift while the rest of the project is being set up. The rest of the project involves building a scaffold platform on the seabed that will be able to hold the ship up after itâs been tipped over, and attaching cassions, giant ballast containers that can alternately be filled with water or air to adjust the shipâs buoyancy, to the side of the ship that tipped above the seaâs surface. When everything is in place, cables will slowly pull the above-water side down towards the platform, while the chains will help it twist back into its normal position. Once there, more cassions will be attached to the formerly below-water side, and together all of the cassions will slowly be filled with air, lifting the wrecked ship to its regular floating height. Then other boats can tow the bandaged wreck away from the island to shore.
The simplicity of the concept belies the practical difficulties. While itâs easy to picture the ship rolling over to right itself, itâs really hard to actually accomplish it, which is why no one had bothered before there was such a significant environmental concern. The materials that structure the Concordia were damaged in the wrecking, and have been sitting in an environment they werenât designed for since then. Itâs impossible to measure and calculate all of the variables, both because there are so many and because the ship further decays with every passing day. Salvagers are taking what they think is their best option, hoping that the shipâs hull will survive the twisting and the platform will hold its weight, among countless other factors. Salvage planners are hesitant to put a date on the removal since new considerations come up every day, but with their current timeline theyâre hoping to have it out in a month or two.
Psychology has never fully fit within the framework of empirical science. Because we interface our thoughts through our conscious mind, itâs hard to objectively tell the difference between actual processes and post-hoc interpretations. Just because I tell you I chose the red apple over the green one because I like the color better doesn't mean that's the only, or even the real, reason that went into my decision-making. Even if I'm telling the truth, and that reason is my conscious understanding of why I chose it, you can't know for certain if that is in fact how I came to that decision or if it's just an explanation to go along with it. While that sounds excessively confusing, it actually does turn out that we're not entirely aware of our decision-making processes. No one would describe their thought process like that, because thatâs not how we consciously experience it, but it does seem to be how it happens. To elucidate similar processes that we donât necessarily perceive, researchers use a range of proxy measures, from reaction time to response order to eye movements, which can be objectively measured and used to estimate the process of interest.
Eyetracking is exactly what it sounds like. A camera is set up so that it can very precisely follow the movements of your eyes, and therefore tell what youâre looking at in sharp detail. The technique has been around for decades, but has recently become more popular as the technology and data processing has improved.
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In one recent study researchers used eyetracking during short video clips to differentiate between people with different mental disorders or healthy controls. That makes it really interesting as a potential diagnostic aid; the process, one set up, is entirely automatic, and it can give a diagnosis to a specified degree of uncertainty in 15 minutes. Itâs important to note that in this study, eyetracking was just being used as an independent factor. Researchers feed the data theyâve gathered into an algorithm that picks up on patterns in the groups they define. After it learns those patterns well enough, it can tell you which group it thinks a new person is in based on their eyetracking data. It does this exceptionally well, but not necessarily in a way that means anything for the diagnosis. Altered eye movement patterns are not inherently a symptom of Parkinsonâs or ADHD, they are just convenient data that happen to vary depending on what diagnosis a person has (although researchers are planning on seeing if they can tie eye movements to a source in actual cognitive symptoms). That doesnât mean eyetracking isnât extremely useful or clinical practical, it just means you need to be careful in interpreting it.
These types of proxy measures are also useful for studying non-human organisms, which donât have the confounding factor of consciousness, but also canât speak to tell us what weâre interested in. Eyetracking was recently been used to further clarify what peahens (female peacocks) look for in choosing a mate. Previous research had used behavioral measures on different interventions; cutting off some feathersâ eyes, for example, meant that a peacock was less favored. Eyetracking is a more direct way of determining which qualities are important. Since peacocks attract their mates visually, it makes sense that the most direct research would examine what the peahens are actually looking at. In this case, the researchers found that peahens spend most of their time looking at peacocks to the width of their tail fan, not individual feather's eyes. This isn't a result they could have predicted from the behavioral information; eyetracking opened up a new line of questions that wouldn't have otherwise been revealed.
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The cofounders of UBiome have an intriguing article on Scientific American detailing the problems they faced as a small company trying to conduct legally ethical research on the human biome. The article is even more interesting for the incidental questions it raises on the ethics of human research outside the traditional studies conducted by professional scientists.
Institutional Review Boards (IRBs) were developed to preclude the human rights abuses that sometimes resulted from scientists having free reign in designing and carrying out their research. Theyâre guided by the Belmont Report, written in 1979. It essentially requires that all human research must carefully respect individualâs rights & special needs, be balanced strongly in favor of helping participants, and be fairly distributed in terms of risks and benefits across the population. The rules are quite thorough and err on the side of caution. However, the problem UBiome unearthed is that the definition of âhuman researchâ might need to be updated in light of contemporary science practices & capabilities.
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UBiomeâs lawyers advised that research needs IRB approval if it: receives federal funding, is a clinical trial, or will be published in a peer-reviewed journal. This covers pretty much all âprofessionalâ science. Much of the research in the US today is funded by government institutions like NIH or NSF, because theyâre some of the only organizations with the resources & inclination to cover the costs of contemporary scientific research. The specific clause for clinical research brings pharmaceutical & interested biotech companies under the umbrella of requirements. Finally, peer-reviewed journals are one of the best, most respected ways of sharing your results with the rest of the world. If youâre a scientist looking to do something with your research, youâre going to (try to) publish it in a peer-reviewed journal, which gives it an audience and stamps it with a seal of legitimacy. (These things vary from journal to journal, but âpeer-reviewâ denotes that the research article submitted is critiqued by other researchers familiar with its area, so research that is not well-designed or satisfactorily analyzed wonât be accepted. While it has its weak points, it essentially serves to weed out bad science. Itâs one of the most successful cornerstones of scientific research.) These categories intentionally cover a wide swath to capture any human research that then could have a potential for abuse.
If those requirements are met, there are different âlevelsâ of IRB requirements depending on what the research actually proposes to do. Itâs a very technical process designed to define as explicitly as possible what constitutes concepts like âresearchâ and âinvolving human subjectsâ which seem clear enough until you try to tease apart which studies have the potential to abuse participants and which donât. All in all, they split projects into categories based on whether they actively interact with people, if those people are living, if theyâre collecting any new information, if the information collected can be tied to the people it comes from, if it involves people who are vulnerable in some way, what its context is, if similar research has been conducted before, etc. On the basis of the answers to all of those questions, a project will either be exempt from IRB review, qualify for an expedited IRB review, or require a full IRB review.
Under these guidelines, projects like UBiomeâs (including 23andMe) are exempt. In their most basic conception, they donât meet any of the qualifying standards (theyâre not federally funded, clinical trials, or intended for peer-review). Because theyâre generating a lot of data, though, 23andMe and now UBiome have decided to look into IRB approval so that they can publish any research they conduct. In an unprecedented (though long time coming) move, 23andMe consulted an independent IRB and was granted exemption from review based on the facts that their analysts do not directly interact with participants nor have any of their personal identification information. They developed a new informed consent process for their participants, but nothing really changed about their practices. UBiome doesnât specify in the article or on their site what IRB process the went through, but it itâs likely the same as 23andMe.
So while both companies have technically met their legal requirements (or gone above them, as they point out), these cases raise a lot of questions about the IRB procedure. The research world is definitely changing, and ethical review needs to update with it. In their article, the cofounders of UBiome give a short list of what theyâd like to see in the âIRB 2.0â: a relatively cheap, publicly available âmini-IRBâ that could cover human research in instances that donât require full IRB review (both 23andMe and UBiome had to pay for independent review, since they did not have their own IRB), more transparent IRB protocols (UBiome wanted to be able to see IRB proposals for similar projects in constructing their own), and public input on the development of a new IRB process.
The first concern is legitimate, but tricky. The government required IRB approval, but it doesnât actually provide any IRBs. Many major research organizations, like universities, set up their own with staff & government approval. If an organization doesnât want to maintain its own IRB, or doesnât have the resources (like UBiome), they apply to an independent one. It would certainly facilitate research if the process was less expensive. The review would be just as thorough, but start-ups would be able to get a foot in the door without having to go through UBiomeâs controversial solution, which was to raise funds before any review took place. The authors also lamented the amount of time they devoted to IRB review, but I donât see the need for a change there. In the process of a review, the IRB can outright reject your proposal, which is unlikely if you took the time to fully understand the requirements and explain them in your proposal (as most researchers would), or send it back with comments for revision. If you adequately update your proposal, it can be approved. (There are obviously experiments that would not pass IRB standards, but the application process should make it pretty clear to anyone taking the time to write a proposal that their plan was unacceptable.) We canât make individual IRBs work faster without sacrificing rigorousness, but we could make more IRBs. This could work hand-in-hand with the idea for âmini-IRBs,â which would then relieve the financial and time strain on human biology-oriented start-ups. The flip side, of course, is that more IRBs, even if âmini,â require more funding, especially if they wonât be charging as much. Iâm not familiar enough with litigation over IRB proposals (Iâm assuming the authors meant other researcherâs proposals, and not the working protocols of IRBs, which are available in excruciating detail) to comment on making them available to the public, but scientific research highly values transparency so this seems like a valid point. The call for public involvement in the formation of new IRB procedures, especially highlighting the most relevant groups in contemporary science, is crucial, and I think all of these issues show the need for a discussion & changes.
However, I think the concerns raised go beyond what these companies describe, and to me those are the more problematic ones. First is the fact that while the 23andMeâs or UBiomeâs analysts & researchers may qualify for IRB exemption because they used anonymized data, the company as a whole has access to everything. It may be better practice to require such organizations to receive IRB approval on the basis of the companyâs operations as a whole, while any individual research projects can be exempted (or not) depending on the data they use. Additionally, both 23andMe and UBiome provide (encourage, in UBiomeâs case) analysis for children of essentially any age. There is a massive debate going on the the scientific community right now about genetics research in children, who are a vulnerable group because of their impaired ability to give informed consent. There are good arguments to both sides (and everywhere in between), but UBiome & 23andMe completely sidestep the ethical considerations, and end up erring on the side of abuse. UBiome asks that parents get their childâs assent (a standard practice in research involving intellectually impaired participants, where the participant gives their assent to participate and their guardian gives consent), but oddly only for children over 13, and this still raises questions about the adequacy of informed consent. In order to be ethical, assent from a vulnerable participant must be as informed as possible and uninfluenced by anyone else. Companies like 23andMe and UBiome have no way of verifying that a child assented at all, let alone in a manner up to ethical standards. This is very discomfiting, and I think strengthens the need for organization-wide IRB review. Itâs not all bad, though. Many people who participated in 23andMeâs research surveys were excited to put their data to use, and interested in making that data public. IRBs have so far been concerned with keeping personal data as private as possible, so I think this situation would be an interesting new practicality for them to work out. However, I still think this should be conducted within the context of company-wide IRB review. There just needs to be new considerations for this type of data.
Companies like 23andMe and UBiome open up a new realm of possibilities in research. They require careful consideration (more careful than has so far been done), but they could become immensely useful for their unique data sets and facilitating public interest & participation in science. Iâm excited to see where they go as this kind of technology becomes more available, but for now Iâm wary of their ethics.
All of our units of measurement - a foot, a kilogram, an hour, etc. - were developed centuries ago out of necessity and have since been refined with advancing scientific techniques. Todayâs technological capabilities are vastly more precise than most people need, but crucial for researchers and engineers. For example, it doesnât make much sense to define an hour or second as a division of a day anymore. Our instruments are capable of much finer measures than the inconsistencies in a minute from one day to the next. So, weâve turned to a more reliable, standard definition of a second that relies on physical properties of matter rather than variable large scale properties like the length of a day. The current, technical definition of a second is âthe duration of 9,192,631,770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium 133 atom.â Cesium 133 radiation has nothing inherently to do with time, but itâs behavior is exceptionally regular, so we use it as an accurate clock.
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The other fundamental scientific units - distance, mass, luminous intensity, electric current, amount, and temperature - have been similarly redefined using more precise measures. These fundamental units are the types of unique measurements that can then be used to denote any other measurement, such as how distance (a fundamental unit) and time (a fundamental unit) can be used to express speed (a derived unit). As of today, however, temperature is still missing a definition that relates it directly to its physical source. Temperatureâs current definition uses a property of water (its triple point - the temperature and pressure at which all three phases of gas, liquid, and solid exist simultaneously, which is hard to imagine from everyday life, but does happen) to anchor one fixed point of the temperature scale, the other being absolute zero, where atoms do not move at all. However, as researchers have been expanding work in very hot (like stars) and very cold (near absolute zero) temperatures, theyâre noticing that this scale doesnât quite work. While the triple point of water is a physical property, and scientists have carefully controlled the atomic properties of the water used to create the measurement, itâs simply not reliable enough to provide a really precise definition. Itâs like trying to time an Olympic sprint with a seconds being 1/86400 of the time from one sunrise to the next.
To fix this problem, researchers at the National Physics Laboratory in Britain are developing a new definition of the temperature scale. Theyâre using a small amount of pure argon gas to more closely measure the relationship between the energy of atoms and temperature. Itâs still a work in progress, but theyâve already broken new ground on the precision of the temperature definition. Their new measurement has almost halved the uncertainty or inaccuracy in the previous standard. For a little perspective, the temperature scale most people use in their daily lives is accurate to about 1 to 5 degrees; this one goes to 0.0000007 degrees.
[Image is the instrument used to contain & measure the argon gas, from the National Physics Laboratory's website.]
A recent post on Scientific American's blog looks at the repercussions of the Supreme Court's ruling that human cDNA can be patented. Overall the author agrees with what I described earlier, that cDNA isn't really much different from genetic DNA, but she also goes a little bit further into what this could mean in the real world. In particular, she describes how this could perpetuate some of the problems in the medical world that lead to the BRCA patent lawsuit in the first place, like monopolizing tests and limiting scientific research.
I recently came across Zooniverse, a host for a diverse range of scientific crowdsourcing. The site was started in 2007 to serve a single study and took off once its creators realized their platform was as useful as the data they collected. Through them, you can help out on projects working on anything from marine life to music descriptions to the formation of galaxies.
Previously: Crowdsourcing to find Near-Earth Objects, Crowdsourcing in scientific research
While, by definition, all living things are made up of cells, cells are not the only things theyâre made of. Complex multicellular organisms, like us, have a lot of other parts, including protein scaffolds to hold groups of cells into shape (including the extracellular matrix), water to make our blood liquid, and fatty substances to keep compartments waterproof and separated. Our cells drive everything that happens, but these other substances are just as crucial to our life processes, even if relatively inert.
One of the things cells do is recognize each other. They can tell, for example, if a cell they come across is your own red blood cell or a bacterium that snuck in. They can also tell if the cell is your own red blood cell or someone elseâs, which is why blood types are so important for transfusions. If someone elseâs blood is close enough in the signals your cells look for to identify it to your own, nothing will happen, but if your cells can tell the difference, theyâll attack the transfused blood as an infection. The same is true for organ transplants, except that your cells are even more exacting. The signals your cells look for on organs are much more complex than the ones they look for on blood cells. Thereâs a lot more variation between different people  in how those signals look, meaning itâs a lot more difficult to find an organ thatâs close enough to your own that your body wonât attack it. That specificity is why we have things like the National Marrow Donor Program.
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Because organ donation is so difficult, it would be fantastic if we could get around it. That would mean that doctors could replace a malfunctioning organ with a new one made up of your own cells. Since theyâre physically your own cells, they have your exact identification signals, and thereâs no need to worry about the transplant being rejected. The obvious problem with this approach is that our bodies donât just grow new organs. When theyâre very young, our cells are unspecialized, and can become any type of cell we need. Those are stem cells. As our bodies develop, the stem cells specialize and lose their ability to form different kinds of cells. As a result, we canât just take some skin cells and move them into a kidney and expect them to re-specialize and function like kidney cells.
Embryonic stem cells, the most famous ones, are found in very young fetuses and can develop into any cell in our bodies (all of our adult cells were once a limited number of embryonic stem cells). While adults do still have stem cell reserves, theyâre in small amounts and already somewhat specialized, and so far scientists havenât been able to grow them outside the body as well as theyâd like. Recently, however, scientists have worked out a process that can turn certain types of our specialized, adult cells, called fibroblasts, into what are called induced pluripotent stem cells. This is amazing. We can now (rudimentarily, but weâre getting there) take cells from under the skin, put them through this process, expose them to factors that tell the new cells they should become trachea cells, and they will.
The problem is all those important things besides the cells themselves. We can grow trachea cells, but we canât grow a whole trachea. Thatâs where this cutting-edge research comes in. With traditional mold-based processes or more modern 3D printing, researchers can custom build synthetic scaffolds to provide a starting point for the new organ. This has been particularly successful with tracheas and bladders - relatively simple, hollow organs. In another approach, scientists have developed a very delicate process that allows them to remove all of the cells from a donated organ without damaging the rest of the structure. Instead of printing a synthetic scaffold, this process uses a biological one, which can then be seeded with the newly grown stem cells. Researchers are trying to get this process working for complex organs like the heart, where synthetic printing doesnât work. Itâs still very difficult because part of the complexity in these organs is in their cells. Hearts have muscle cells, nerve cells, regulatory cells, and more, that all have to be in exactly the right place and function in exactly the right way in order for the heart to do its job.
Itâs a difficult project, but in the end it will mean we no longer need to closely match donor organs to recipients. Instead, weâll be able to either print our own organ or use only the non-cellular components of a donor organ. This will completely revolutionize organ transplants, and relieve the incredible stress put on the current system with waiting lists, testing potential donors, and time-sensitive organ transportation.
[First image is an illustration of cells within the extracellular matrix from the University of Michigan; second is from the Ott Lab at Harvard University & Massachusetts General Hospital, where a lot of this research is going on.]
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This Scientific American article highlights an interesting discovery that qualifies a longstanding aspect of autism. Theory of mind is the ability to understand another personâs perspective as separate from your own. People usually develop theory of mind around age three, and psychologists have developed a standard task to give children to see where they stand on this ability, called the Sally-Ann test. In this test, a child watches the researcher play with the dolls Sally and Ann (or researchers play their roles). Together, Sally and Ann put a toy in a bowl. Then Sally leaves the room, and Ann moves the toy to a box. Sally comes back, and the child is asked where she will look for the toy. If the child can understand that Sallyâs understanding is different, that even though s/he knows the toy is in the box, Sally doesn't know it was moved, so she will look in the bowl. If the child doesnât have theory of mind, s/he will choose the box, because thatâs where s/he would look for the toy. Children with autism are substantially older when they show theory of mind (via the Sally-Ann test or other, similar versions for adults).
However, the researchers in this study reasoned that this test might have a flaw when it comes to autistic children. One of the salient points of autism is a disinterest in social interactions. Since the Sally-Ann test is solely motivated by social interactions (with the researcher or the dolls), it could be that the children with autism have less motivation to perform the task, not that they donât have theory of mind. The researchers compared normally developing and autistic childrenâs performances on the Sally-Ann test and a similar, but importantly modified, task called the Dot-Midge test. In this test, the child is competing with Dot and Midge (dolls or researchers) to win the toy. Dot an Midge act the same way as Sally and Ann - they both put the toy in a bowl, then Midge leaves, and Dot moves it to a box. Then Midge comes back, and the three (Dot, Midge, and the child) take turns guessing where the toy is. Whoever guesses right gets to keep it. Crucially, the child guesses second, and gets to chose who goes first. If s/he has theory of mind and is motivated by the competition of the game, the child will pick Midge to go first, since she doesnât know the toy was moved and will guess the wrong spot, allowing the child to win the toy. The researchers found that while very few of the autistic children passed the Sally-Ann test, almost three-quarters passed the Dot-Midge test, suggesting that autistic children do actually gain theory of mind at a similar age as normally developing children.
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This is interesting and practical knowledge that will help hone our understanding of and interventions with autism, but it also exposes one of psychological testingâs deepest flaws. Psychology comes up with theories that explain behavioral phenomena in humans - young children donât understand othersâ perspectives, so we sometimes see them acting in ways that seem strange given that we do understand othersâ perspectives, and we call this understanding theory of mind. Researchers then come up with simplified, controllable ways to test out these theories and learn more about them - they developed the Sally-Ann task. Researchers then use that task as a definitive test for the theory - if a child fails the Sally-Ann test, he or she does not have theory of mind.
The problem is that these tests are developed somewhat in isolation. If theory of mind was the only thing that varied in children than the Sally-Ann test would be a perfect measure of it. But, of course, there are other psychological differences, and some of them can impact what answer a child gives, independently of their theory of mind capability. In the study described in the Scientific American article, the researchers show that a number of autistic children who fail the Sally-Ann test do, in fact, have theory of mind, they just donât apply it to the Sally-Ann test because theyâre not motivated by its social incentive. Rather than giving a definitive yes-no insight on a childâs theory of mind, the Sally-Ann test actually gives the cumulative result of an interaction between theory of mind and social motivation, and probably other factors as well. Because social motivation was assumed as a given by the researchers who developed the Sally-Ann test, so no considerations were made for it. In normally developing children that might not matter, but itâs very important in autistic children. Because psychological tests are so hard to control - developers can only account for the factors they know of and consider important, and thereâs no way to physically determine them - they are susceptible to problematic confounds.
Researchers are aware of this limitation - the point of this study was to show that social motivation was in fact a confounding factor for the Sally-Ann test - but itâs important to remember that many psychological theories are more conceptually useful scaffolding than concrete facts about how our minds work.
Update: optogenetics used to relieve OCD behaviors in mice
In this fairly recent Science paper, the researchers used optogenetic control in a genetically-mutated mouse to relieve the mouse version of obsessive compulsive disorder (there's also a less-technical overview of it on Scientific American). These mice are a special type that are missing the gene SAPAP3, which creates problems in communication between certain neurons on the cellular end and leads to increased anxiety and compulsive grooming on the behavioral end. Because of this, they're used as a proxy for OCD. Since scientists know exactly what the mutation is doing and where, these researchers developed a study to see if they could counter the neural signaling defects with optogenetic control. They selectively stimulated the area of the brain that was affected by not having SAPAP3 and found that those mice stopped compulsively grooming so much, along with restoring some of the normal neuron communication patterns.