Showing posts with label space-science. Show all posts
Showing posts with label space-science. Show all posts

October 2, 2017

Pseudo-Heliocentric Readership Information in Gravitationally Bound Form

Or, how to get 300,000 reads by being persistent [1] and getting results in unexpected places. Let's review our milestones in three cartoons.






The made-up planetary orbits featured here [2] may violate the physics of actual solar system orbits, at least as simulated by Super Planet Crash [3].


NOTES:
[1] Candy, A. (2011). The 8 Habits of Highly Effective Bloggers. Copyblogger, October 25.

[2] Previous readership milestones, in order of distance from central star: 20000, 50000, 100000 (first image), 120000, 150000 (second image), 200000, 250000 (third image).

[3] Featured in the Scientific Bytes and Pieces, August 2015 post.


August 26, 2015

Scientific Bytes and Pieces, August 2015

Welcome to this month's version of Scientific Bytes and Pieces. The first feature is a sad note: complexity theorist John Holland has passed away at the age of 86. The father of genetic algorithms and a pioneer in the field of complex adaptive systems, Holland's contributions will live on. Here are two obituaries: one from the New York Times and another from the Washington Post (written by Holand's colleague Scott Page).

R,I,P. John Holland. COURTESY: Plexus Institute.

The SAVE/Point collaboration and Stefano Meschiari have developed an interactive game called Super Planet Crash. This "hours-of-fun"-type game simulates the gravitational dynamics of solar systems. Build your own solar system today! The virtual world physics come courtesy of algorithms designed to detect exoplanets.

Screenshot of Super Planet Crash. WARNING: it is not as easy as it looks.

Next up is a recent article from FiveThirtyEight Blog called "Science Isn't Broken". Despite the sizable body of blog posts and articles lamenting the "brokenness" of the modern scientific enterprise, it turns out that such fears are misplaced. As it turns out, science is a hard enterprise, and prone to error, unexpectedness, and revision. Since I believe that couching these realities as symptoms of dysfunction does the scientific community more harm than good, this discussion is a welcome contribution to our understanding of how science is done.

Interestingly, whenever the topic of "broken science" comes up, cognitive biases are almost never mentioned. Yet cognitive biases play an integral role in decision-making and interpretation. Even algorithms have been shown to exhibit significant social bias. Jim Davies offers us an article via Nautil.us called "Why You’re Biased About Being Biased" in which he reviews the state of cognitive bias research. An accessible tour of the field as well as food for thought (and reevaluation of those thoughts).

Another reason why science is hard rather than broken is the existance of chaotic behavior. Strange and unpredictable phenomena such as transient chaos challenge the expectations and arguments of the "science is broken" crowd. Some people, such as Tamas Tel, find joy in these types of phenomena. See the recent Chaos article "The Joy of Transient Chaos" for this perspective. While not particularly accessible to a popular science audience, the article should give you a glimpse into an alternate perspective.

An artistic take on a series of hyperlinked documents. COURTESY: boingboing.net.

Despite the hard nature of the scientific enterprise, every once in a while breakthroughs are made. This year is a milstone for several of these. The word "hypertext" is 50 years old, and the Einstein's publication on General Relativity is 100 years old. On a related note, Einstein's "Annus Mirabilis" was 110 years ago this year. So much for broken science.

Following-up on a previous Synthetic Daisies post about Theory Hackathons, here is an article that makes the case for hackers to support the cause of scientific data analysis. While the focus is on taming the glut of Neuroscience data, the same principle would apply to all large-scale data. Can hackers help to make sense of data and can they help us bridge the gulf between data and theory? Perhaps we will discuss this in a future post.

July 26, 2015

Having a Positive Celestial Body Image is Important

Lots of planetary science news in the last few weeks. Between the arrival of the New Horizons probe at the Pluto mini-system and the discovery of the Kepler-452b exoplanet, lots of great pictures to behold. And as is often the case, space science leads to greater knowledge about our own planet, but more about that at the end of the post.

As the New Horizons probe approached Pluto, we began to gain an appreciation for this far-flung corner of the solar system. This includes the planet itself, which may exhibit Nitrogen cycling between its atmosphere and surface glaciers.



The anticipation builds as one zooms in. COURTESY: Discovery News.

Not only do we have an up-close accounting of Pluto's surface, we also gained knowledge about Pluto's environs, which consists of a number of celestial bodies. The two main bodies are Pluto and its main moon Charon. Notably, Pluto and Charon orbit a common center-of-gravity, which is a bit different from the relationship between Earth and the Moon.


Map of the Pluto mini-system (top) and the tidal locking between Pluto and Charon (bottom). TOP: IAU. BOTTOM: Stephanie Hoover, Wikimedia Commons.

While the discovery of exoplanets is no longer news, ones that resemble Earth still cause people to stand up and take notice. The latest exoplanet discovery is called Kepler-452b, which is within the circumstellar habitable zone of Kepler-186. 




Diagram and artist's renditions of Kepler-452b, the latest and greatest earth-like exoplanet. COURTESY: Space.com.

Finally, I would be remiss if I did not mention the possibility of an intense El Nino this coming year and the associated climatological modeling. 

Comparing powerful El Nino events: 1997-1998 and (coming soon?) 2015-2016. COURTESY: NOAA.


May 25, 2015

Scientific Bytes and Pieces, May 2015

Bytes and Pieces is a collection of links and essays recently enncountered from across the internet, consisting mainly of scientific essays and applications.


Asterank: A web-based interface which visualizes all of the asteroids in our solar system and ranks them according to economic utility (e.g. asteroid mining). Thus, Asterank combines physical science with an optimistic futurism. See the associated Github repository for technical details.

Screenshot of Asterank Interface.


The Scientific Method is an Idea Ready for Retirement. Despite the provocative stance, this is indeed the view of one systems-level thinker (Melanie Swan) who argues against the power of reductionist hypothesis-testing in a high-throughput, multivariate world.


Writing at Nautil.us blog, Sam Arbesman brings us a tour of "robust yet fragile" systems. This essay explores the consequences and by-products of kludgeiness in complex systems. The "crawling horrors" that Arbesman refers to are small-scale errors that cause failures in systems that are otherwise error-tolerant.


Making Espresso In (Outer) Space. An Italian coffee company (LavAzza) is behind an effort to make Espressos in space (e.g. zero-gravity conditions on the ISS). Looks like a challenge to both make and drink enjoyably, although without gravity one does not have much of a choice. Next up on the exotic coffee wishlist: leveraging quantum foam to make yoctolattes.

The glamour and impracticality of old-fashioned space coffee.

Preparing a cup (or rather a pouch).

Not quite as advertised, but she will enjoy it!

Via Singularity Hub, we learn of Second Life founder Philip Rosedale's latest efforts: to build a virtual metaverse at the scale of planetary communities. The proposed platform (High Fidelity) would be an open-source virtual reality-based social network with a variety of potential uses. A planetary-scale metaverse will require large-scale, coordinated, three-dimensional computing resources, which means that this vision should be quite the technical challenge to realize.

High Fidelity wants you! As a technical expert and eventually a user, but still...


January 26, 2015

Science and Politics or Science versus Politics?

A few items on the intersection of politics and science (and the tension between the two). First up is an infographic that shows the relative frequency of various "science and engineering words" during the annual State of the Union (SOTU) address by all US Presidents since Teddy Roosevelt. The "science and tech" category is at the bottom, and has been an increasingly important component of these speeches over the last 40 years.


Related to societal relevance is the whole issue of political will and action on science-related topics. This is particularly true when it comes to policies that address Anthropogenic Global Warming (AGW). This point was not missed during the 2015 SOTU. However, one might wonder how effectively climate policy can be when most politicians have a cursory (at best) technical understanding of scientific issues. Perhaps advocacy for science policy (e.g. lobbying) is not enough after all -- perhaps we need more scientist-politicians.

COURTESY: 350.org

Many discussions of global warming (mostly involving denialists) involve an appeal to the scientific consensus. While the consensus does point strongly towards the reality of a human-induced warming of the planet, the discoveries that lead to this consensus were individualistic quests for data. The data were not voted into existance, and neither can consensus on a scientific issue [1]. While skepticism should come into play when considering the implications of findings, it should not play a role in judging conclusions drawn from isolated findings. For one example, please see this article by Ethan Siegel on Starts With a Bang! blog on why science by democracy (or popular consensus) does not represent how science is actually done.

A call for scientist-politicians? COURTESY: Grady Carter blog (for the montage).

The final item in this post in a new Kickstarter/film initiative to bring awareness to the American space program. "Fight for Space" is a project to bring awareness of budgetary cuts to our scientific endeavors and the pressure to fulfill politically-approved missions. To change this state of affairs, check out the Planetary Society's advocacy efforts. The scientific mission of NASA has been yielding significant returns as of late [2], so help to keep this momentum going.

COURTESY: SaganSense Tumblr.

NOTES:
[1] The popularity of a set of ideas do not mean that they are scientifically credible. For more, see this article from Why Evolution is True regarding the lack of evidence for but popular persistence of proposals involving a divine origin of life.



January 5, 2015

The Flow of Time, Science, and Archives

Here are a few milestones and interesting items to report for the New Year:

2014 was a good year for both space science and science in general. It's safe to say that the biggest story in science for 2014 was the successful landing of a probe (the Philae lander) on the surface of a comet (67p) by the European Space Agency. But the year was also not without dissapointments. Overall, many breakthrough findings and excellent papers occured in a number of fields. In the years ahead, it will be interesting to see what kinds of advances are made in 2015 from emerging work done during 2014.

If you are tired of celebrating another New Year according to the Gregorian calendar, here is an article from Futurity to make you consider an alternative. While the focus in this article is on the Hanke-Henry Permenant Calendar, there indeed is more than one way of dividing up the time it takes our planet to make a complete revolution around the Sun. This may or may not include calendars from other cultures, of course.

First milestone: The 24-year-old preprint server [1] arXiv published its one millionth (10^6th) paper on December 29, just in time for the new year. Despite being around for a quarter century, arXiv has become the template for an open access publishing revolution. Originally founded by Paul Ginsparg in 1991 [2], the bulk of the million paper total reflects impressive growth in the past several years.

The lifespan of the arXiv in terms of growth over time and abundance of articles by field. COURTESY: arXiv and [2].

Second milestone: By the end of Monday, January 5th, Synthetic Daisies will have reached 120,000 readers. Much like the arXiv, the bulk of this growth has occured in the last few years. The blog was started in December, 2008, so I also wish the blog a Happy 6th Birthday [3].


NOTES:
[1] Tomaiuolo, N.G. and Packer, J.G.   Pushing the Envelope of Electronic Scholarly Publishing. Searcher, 8(9), October (2000).

[2] Ginsparg, P.   arXiv at 20. Nature, 476, 145-147 (2011).

[3] Is this actually possible, or is it more like worshipping a fetish? I guess for purposes of good form, I should create an avatar that represents "the blog".



June 27, 2014

Historical Contingencies at the Birthday Party

Historical contingencies are perhaps the most interesting outcomes of the evolutionary process. Stephen J. Gould spent a lot of time and energy making this idea popular, but evidence comes from both paleontology [1], extant populations [2], and experimental evolution [3]. However, the ubiquity of the contingency concept does not resolve its phylogenetic consequences. Is historical contingency highly specific (a hard constraint resulting in unique paths), or is it a softer constraint? And how can we understand the role of convergent evolution within this framework? We will approach this from a mathematical perspective, and answer the riddle of what evolution and birthdays have in common.


Definition of generative science (Wikipedia) and historical science (RationalWiki). 

Evolutionary Histories and Their Accidents
Like human history, evolutionary history is a product of many forces and causes. We often think of these factors as a series of chance events (sometimes unique) that lead to a given outcome [5]. Observers sometimes use this point to argue that history is not systematic and thus cannot be separated from context (and thus comparative history would be quite impossible) [5]. But this also assumes that the factors that make a given evolutionary history unique (its branching events) are "hard". Not only are they irreversible, but also should not have significant similarities. The outcomes of the evolutionary process (genotypes and phenotypes) are locked in to a specific trajectory. By itself, this constraint should favor some changes over others and disallow changes that resemble even closely-related lineages.

If historical contingency is a hard constraint, then this leads us to an evolutionary hypothesis: historical contingency creates irreversible paths to highly-unique phenotypes. While a bit simplistic, this nonetheless serves to understand the consequences of contingency. Recall that the evolutionary process occurs through branching, and results in a series of evolutionary outcomes (Figure 1). While these outcomes are individually different, their degree of uniqueness relies on the "hardness" of the branch that separates one outcome from another. Figure 1 not only shows the results of branching, but also assumes "hard" constraints. The contingencies generated by this model involve hard constraints that results in a unique, lineage-specific partition of the search space.

Figure 1. An example of a phylogeny with unique, non-recurrent evolutionary outcomes. The evolutionary changes act as hard constraints, and each terminal taxon occupies a distinct 1-dimensional subspace. 

In Figure 1, a conventional phylogenetic model demonstrates how a search space can be partitioned through evolutionary branching processes. However, when the constraints are softer, each branching event results in less distinction between the resulting alternative forms and increases the chances that traits or forms that resemble those of a related lineage (even distantly so) will emerge. Figure 2 demonstrates this difference using the analogy of the Plinko game [6]. In this case, the combination of the process and outcome of contingency creates an overlapping search space over time for a given lineage (see the distribution of Plinko balls at the bottom of Figure 2). 

Contingency also rests on the assumption that evolutionary randomness results in unique combinations of traits. One feature of historical contingency involves building upon previously-acquired traits. As complexity is built in this way, the total number of possibilities decreases. But while the stochastic nature of evolution is a matter of conditioned chance, branching is an assumption of theoretical intuition. Therefore, evolutionary outcomes can converge even when their forms nominally exist in different lineages. But given these constraints, shouldn't convergent evolution be impossible? Before we answer the question (and the answer is no) we must take an intellectual detour by way of birthday parties.

Figure 2. What it means to have an overlapping space of evolutionary outcomes enabled by soft historical constraints. COURTESY: Plinko Probability, version 2.02. PhET Interactive Simulations.


How are birthday parties at all relevant here? The birthday party paradox, a statistical curiosity, might help us establish a link between contingency and recurrence. But first, let us revisit our evolutionary process-as-hierarchical tree model. In this model, all possible combinations of n are classified using a tree-like structure. Given that the search space is much larger than the number of objects being classified, do they also end up in unique categories? Perhaps. But, as we will learn, it may not matter as much as does the size and complexity of the evolutionary landscape itself.

What is the Birthday Party paradox [7]? Amazingly, this did not make a Quora list of the most counterintuitive mathematical results [8]. But perhaps this result is not so intuitive after all. Say you were to survey a room of n people. Given that every day of the year has an equal chance of being a birthday, how many people will you need to sample in order to find at least two people with the same birthday? The answer you might give depends on your intuitions about randomness. With 365 days in a typical year, one might assume that you would need a lecture hall of at least 300 people. But in fact, once you reach a sample size of 47, the probability (95%) becomes asymptotic to 100%. See Figure 2 for a graphical representation.


Figure 2. Number of people surveyed (x-axis) vs. probability of at least two people having the same birthday (y-axis).

Evolutionary Histories and Their Coincidents
This outcome results from a mathematical principle called recurrence. This principle suggests that motifs and themes can recur at an unknown frequency -- it explains why you get runs of heads or tails in a series of coin flips. This recurrence has nothing to do with the outcomes being related to one another. They are merely conincidences inherent in a generative process. In the evolutionary outcome space example, this suggest that overlap can occur in the form of deep similarities. Can this be applied to the probability that n lineages will exhibit convergence?

Not exactly what we are talking about here, but an evolutionary birthday nonetheless.

Phylogenetic birthday (or contingency) paradox:
In the next few tables, I have shown how the mathematics and problem formulation of the standard birthday paradox can be used to understand a generative set of evolutionary configuration and the probability of a parallel evolutionary outcome. 

What the data should look like (standard Birthday Party paradox):

 What the data should look like (proposed evolutionary paradox):

In the case of the evolutionary paradox, an exceedingly small sample size of 60 possible configurations was used for demonstration purposes. It is of note that this model is scalable to very large numbers of distinct evolutionary configurations. However, it is clear that the probability of convergent evolution is nearly 100% well before a given lineage is locked in to a single point in the configuration space. As the number of changes increases, the number of possible configurations changes is correspondingly reduced. 

But....but.....there are assumptions!
This model makes a few general assumptions. One, while each change is assumed to be countable, there is no accounting of how hard or soft the constraint actually is. This could be resolved through using a soft classifier to characterize each change, although would not remove the effects of geographically-localized specialization. An example of this is in the supplemental Excel dataset (see Notes section below). Another is that all evolutionary configurations are countable in the same way (e.g. no modularity). Again, this can be resolved by generating a matrix for each component of an organism (e.g. phenotypic module). 

Despite these assumptions (for better or for worse), the general principle of recurrence should give us a somewhat useful model for estimating how plausible or implausible convergent evolution is for a given set of evolutionary relationships. Recurrence is a useful tool that is largely ignored in conventional discussions about evolutionary constraints and parallel evolution. Once again, recurrence (by way of Henri Poincare in Figure 3) allows us to use principles of complexity theory to better understand evolutionary phenomena [9].


Figure 3. An example of Poincare recurrence. In this example, an image of Henri Poincare has been permutated, with reconstruction of the original image (or a reasonable approximation) is reached well before the maximum number of possible combinations is reached.


UPDATE (6/30/2014):
It was pointed out to me by a reader that birthdays have a distribution of their own throughout the course of a year. For example, birthdates in the Summer months (June, July) are more common than those in the winter months. This is of course due to human mating preferences and seasonality (and so birthdays are actually a quasi-stochastic process). Hence, there is a clustering of more common (as opposed to less common) birthdates on the calendar (Figure 4).

Figure 4. Visualization of birthdate frequency (in heatmap form) distributed across the calendar year. COURTESY: VizWiz blog and NYTimes.

I imagine this type of probability density is also somewhat true for evolutionary data across the diversity of a genus, order, or domain. But this type of clustering is also an outcome of stochastic processes (and one reason why recurrence is possible). When sampled at a given point in time, the outcome of a stochastic process is often not uniformly distributed -- in fact, it reveals clusters which must be distinguished from clusters that result from non-random processes. The question would be whether or not birthdates (or confounding evolutionary processes) cluster so significantly as to override clusters that result from randomness. The birthday paradox equations don't explicitly take that into account, but that likely does not invalidate the larger pattern.

UPDATE (8/4/2014):
Here is a good recent article from Nautil.us Magazine on evolutionary contingency. Puts a lot of the contemporary support for the idea in perspective.

Zorich, Z.   If the World Began Again, Would Life as We Know It Exist? Nautil.us, June 19 (2014).


NOTES:
Mathematical notation courtesy Wolfram MathWorld (http://mathworld.wolfram.com). Implemented in Excel courtesy of eXcel eXchange (http://excelexchange.com). Excel workbook (computed using pseudo-data) located on Github (https://github.com/balicea/evo-birthdays).

[1] Vermeij, G.J.   Historical contingency and the purported uniqueness of evolutionary innovations. PNAS, 103(6), 1804-1809 (2006).

[2] Taylor, E.B. and McPhail, J.D.   Historical contingency and ecological determinism interact to prime speciation in sticklebacks, Gasterosteus. Proceedings of The Royal Society of London B, 267, 2375-2384 (2000).

[3] Blount, Z.D., Borland, C.Z., and Lenski, R.E.   Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. PNAS, 105(23), 7899-7906 (2008).

[4] Travisano, M., Mongold, J.A., Bennett, A.F., and Lenski, R.E.   Experimental Tests of the Roles of Adaptation, Chance, and History in Evolution. Science, 267, 87-90 (1995).

[5] Fales, E.   Uniqueness and Historical Laws. Philosophy of Science, 47(2), 260-276 (1980).

[6] The Plinko analogy has also been used to describe the epigenetic landscapes of Waddington: Gordon, R. Introduction to differentiation waves Part 2. The evo-devo of epigenetic landscapes as differentiation trees. Embryogenesis Explained course (2013).

[7] Fletcher, J.   The Birthday Paradox at the World Cup. BBC News Magazine, June 15 (2014).

[8] Mathematics: what are some of the most counterintuitive mathematical results? Quora, March 27 (2014).

[9] Crutchfield, J., Farmer, J.D., Packard, N.H., and Shaw, R.S.   Chaos. Scientific American, December (1986).

June 9, 2014

The Final Phase of Starstuff

Everything must go (to starstuff)! Below are the final two sets (XII and XIII) of supplements for the Cosmos reboot, cross-posted as always to Tumbld Thoughts. Enjoy!

XII. Changing the World, One Carbon Sink at a Time.

 
Here are the supplemental readings for the twelfth episode of the Cosmos reboot. This episode, called "The World Set Free", is a point-by-point refutation of climate change denial. Also features a trip to Venus (below are an easter egg and a fictitious Venus-Earth mashup). Readings are organized by theme.


Venus and the case of the the Runaway Greenhouse:
Carl Sagan and the Quest for Life in the Universe, Cosmic Horizons, American Museum of Natural History.


Billings, L.   Fact or Fiction? We can push the planet into a runaway greenhouse apocalypse. Scientific American, July 31 (2013).

Kunzig, R.   Will Earth's Ocean Boil Away? National Geographic, July 29 (2013).


Sir, Don't Forget Your (climate) Change!


Carbon Budget, Learn Bazaar.


A limit on CO2 Drawdown. Nature, July 2 (2009).

Glikson, A.   No alternative to atmospheric CO2 drawdown. Skeptical Science blog, February 14 (2013).

Vidal, J.   Geoengineering side effects could be potentially disastrous, research shows. The Guardian, February 25 (2014).


Weather, Climate, and Models:
What's the Difference Between Weather and Climate? NASA Mission Pages, February 1 (2005).


A Breathing Earth. UX Blog, July 29 (2013).

Downscaling Climate Data. Climate-Decisions.org.


Our Boundless Energy Future:
Naam, R.   Smaller, Cheaper, Faster: does Moore's Law apply to solar cells? Scientific American guest blog, March 16 (2011).

Auguste Mouchot and his solar engine. Land Art Generator Initiative.

Alicea, B.   Solar is at a cost-per-unit threshold! Tumbld Thoughts blog, April 23 (2014).

Frank Shuman. Encyclopedia of Earth.

History of Solar Energy. SolarEnergy.com


Teller, A.   Google X Head on Moonshots: 10X Is Easier Than 10 Percent. Wired, February 11 (2013).

  

XIII. Goodbye and Goodnight, even when there is no sun to set.


Here is the thirteenth (and final) installment of the supplemental readings for the Cosmos reboot ("Unafraid of the Dark"). Readings are (as always) organized by theme. 


Information, Information Everywhere
Chesser, P.   The Burning of the Library of Alexandria. eHistory Archive, June 1 (2002).

Size of the Internet. Wolfram|Alpha.

Moskvitch, K.   Paradox Solved? How Information Can Escape from a Black Hole. Space.com, March 4 (2014).


Expanding your Worldview
Erdapfel and Early World Maps, Wikipedia.


Alicea, B.  Plausibility and de Navitus Models of Complex Systems. Synthetic Daisies blog, March 21 (2013).


The Galactic Circus
Neutron Stars and Pulsars. NASA Goddard Space Flight Center. Picture courtesy Universe Today.

Dark Energy, Dark Matter. NASA Science: Astrophysics. 


Astrobio   New Information about ‘Snowball Earth’ Period. Astrobio.net, March 3 (2013).

Dell'Amore, C.   "Snowball Earth" Confirmed: Ice Covered Equator. National Geographic, March 4 (2010).

Alicea, B.   On Bet Hedging and Evolutionary Futures. Synthetic Daisies blog, January 24 (2014).

A Pale Blue Dot. The Planetary Society.



Voyager has left the building (Solar System):
Voyager I. xkcd blog, #1189, March 22 (2013). Explain xkcd wiki. 


Witze, A.   First hints of waves on Titan's seas. Nature News and Comment, March 17 (2014).

The Heliosphere. Cosmicopia, NASA.

Benningfield, D.   Manganese Nodules. Science and the Sea, October 25 (2009).





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