June 30, 2015

Posters at the International C. elegans Meeting

UCLA and Los Angeles. COURTESY: UCLA Department of Physiology.

I just returned from the International C. elegans Meeting in Los Angeles (being hosted on the UCLA campus). There are posters, talks, workshops, and much fun to be had. I will give a more detailed discussion of some of the sessions in a future post.

Some people (not me) took turns wearing the "worm suit".

There were several days of talks and posters, plus the famous C. elegans art and variety shows. Talks ranged from Physiology to Evolution and Development. The worm art show is somewhat unique to the conference, The OpenWorm group was able to meet up and discuss research strategies. 

There was also a worm art show. Here are some of the entries. 

Aside form partaking in the intellectual and social festivities, I also presented two posters on Saturday night. One was in the area of experimental evolution, and the other on the DevoWorm project.

Sample of the Experimental Evolution poster. Full poster can be viewed/downloaded here.

Sample of the DevoWorm poster. Full poster can be viewed/downloaded here.

My week was not all worm biology. I also sampled some botany, courtesy of the Mildred Mathias Botanical Garden, UCLA.

June 17, 2015

Breaking the Threshold of 150,000 Reads

Great news! According to Blogger analytics, Synthetic Daisies blog has just surpassed 150,000 reads! This calls for a milestone post -- as a cake with candles would be logistically and conceptually difficult. In addition, Synthetic Daisies now has 300+ posts in the archives.

Most recent logo design, trite subtitle.

When I started Synthetic Daisies, it was loosely modeled on a style typical of the science blogosphere in 2008 (with a bit more casual approach). I was also (and have been since the late-90s) inspired by what Wired's approach to web content. This landscape has changed quite a bit, and so has Synthetic Daisies. Having my own blog has allowed me to address my own set of interests in my own style. I've also been presented with unique opportunities for scholarship which are not typically "blog-like", but interesting nonetheless.

Allowing myself to be myself since December 2008.

Finally, aside from the ten pages hosted here, the nine most read posts (circa June 2015, courtesy Blogger Analytics) are as follows:
Post Name







Theoretical Essay



Theoretical Essay

June 11, 2015

Slipping Down the Fluid Slope of Ethical Integrity

This post will focus in on the slippery slope of research ethics, particularly the consequences of strange things happening in the course of pursuing one's best intentions. Cheeky images and puns will help to accentuate the story.

I have been leery of the start-up Uber ever since I heard stories about their varied ethical breaches [1], but now I'm even more deeply skeptical. Uber is showing exactly what can be accomplished when the "technically not illegal" ethos runs amok. Apparently, the ridesharing service entered into a research partnership with Carnegie Mellon, only to poach massive amounts of staff at-will [2]. As I understand it, the reason for this is largely superfluous. Uber wanted to possess expertise in Artificial Intelligence and automation, but did not want to go through an intermediary. Generally speaking, academic-private sector partnerships are not supposed to work like patent troll litigation. But Uber is a wildly-successful startup, so some non-zero percentage of the population are sure to overlook the ethical lapses.

Not illegal, not illegal....the Uber business model? REFERENCE: Family Guy.

Another example of the ethical slippery slope comes from the open-access journal troll and Alan Sokal wannabe John Bohannon. As a feature writer for the journal Science, he once did an updated version of the Sokal hoax where nonsensical papers were sent to a large number of open-access journals. The catch is that some of the journals published the articles for little more than a publication fee (and minimum editorial oversight) [3]. More recently, a new hoax involved an intentionally shady study that touted the health benefits of chocolate [4]. The thing is, the popular press picked up on the paper before it could be retracted. Awesomely delicious stuff (pun intended). The chocolate study has ignited a debate in the world of internet opinion, both in support and as criticism. Aside from the rhetorical point that provocative results can often result from p-value hacking [6], the most obvious problem is that you are intentionally drawing questionable conclusions and having them published. Even though an important point is made, the purposeful dissemination of false findings can lead to serious unintended consequence [7]. In any case, I suppose if the pages of Science ever see a high-profile paper retraction [8], Bohannon's team will get right on the case.

The iffy ethics of sting operations against questionable peer-review processes and journalistic hype machines. REFERENCE: Willy Wonka and the Chocolate Factory.

[1] Newton, C.   This is Uber's playbook for sabotaging Lyft. The Verge, August 26 (2014).

[2] Lowensohn, J.   Uber gutted Carnegie Mellon's top robotics lab to build self-driving cars. The Verge May 19 (2015).

[3] Alicea, B.   Fireside Science: the Consensus-Novelty Dampening. Synthetic Daisies blog, October 22 (2013).

[4] Bastian, H.   Tricked: the ethical slipperiness of hoaxes. Absolutely Maybe blog, May 31 (2015).

[5] Gelman, A.   John Bohannon’s chocolate-and-weight-loss hoax study actually understates the problems with standard p-value scientific practice. Statistical Modeling, Causal Inference, and Social Science blog, May 29 (2015).

[6] Kassel, M.   John Bohannon's Chocolate Hoax and the Spread of Misinformation. Observer.com, June 6 (2015).

[7] Data “were destroyed due to privacy/confidentiality requirements,” says co-author of retracted gay canvassing study. Retraction Watch blog (2015).

May 31, 2015

Kuhnian Practice as a Logical Reformulation

Are 01110000 01100001 01110010 01100001 [1] shifts a loss, a gain, a mismatch, or an opportunity for intellectual integration and the birth of a new field?

In the Kuhnian [2] approach to empiricism, a well-known outcome observed across the history of science is the "paradigm shift". This occurs when a landmark finding shifts our pre-existing models of a given natural phenomenon. One example of this: Darwin's finches and their evolutionary history in the Galapagos. In this case, a model system confirmed previous intuitions and overturned old facts in a short period of time (hence the idea of a scientific revolution). 

During a recent lecture by W. Ford Doolittle at the Insititute for Genomic Biology, I was introduced to a term called "Kuhn loss" [3]. Kuhn loss refers to the loss of accumulated knowledge due to a conceptual shift in a certain field. One might consider this to be a matter of housecleaning, or a matter of throwing out the baby with the bathwater. The context of this introduction was the debate between evolutionary genomicists [4] and the ENCODE consortium over the extent and nature of junk DNA. During the talk, Ford Doolittle presented the definitions of genome function proposed by the ENCODE consortium as a paradigm shift. The deeper intellectual history of biological function would suggest that indeed junk DNA not only exists, but requires a multidisciplinary and substantial set of results to overturn. Thus, rather than viewing the ENCODE results [5] as a paradigm shift, it can be viewed as a form of intellectual loss. The loss, paradigmatic or otherwise, provides us with a less satisfying and robust explanation than was previously the case.

A poster of the talk. COURTESY: IGB, University of Illinois, Urbana-Champaign

Whether or not you agree with Ford Doolittle's views of function, and I am of the opinion that you should, this introduces an interesting PoS issue. In the case of biological function, the caution is against a 'negative' Kuhn loss. But Kuhn loss (in a linear view of historical progress) usually refers to the loss of knowledge associated with folk theories or theories based on limited observational power. In some cases, these limited observations are augmented with deeper intuitive motivations. This type of intuition-guided theory usually becomes untenable given new observations and/or information about the world. Phlogiston theory [6] can be used to illustrate this type of 'positive' Kuhn loss. Quite popular in Ancient Greece and Medivel Europe, phlogiston theory predicts that the physical act of combustion released fire-like elements called phlogistons. Phlogistons operated in a manner opposite of the role we now know oxygen serves in combustion and other chemical reactions. Another less clear-cut example of 'positive' Kuhn loss involves a pre-relativity idea called aether theory predicts that the aether (an all-enveloping medium) is responsible for the propogation of light in space.

In each of these cases, what was lost? Surely the conclusions that arose from a faulty premise needed to be re-examined. A new framework also swept away inadequate concepts (such as "the aether" and "phlogistons"). But there was also a deeper set of logical structures that needed to be reformulated. In phlogiston theory, the direction of causality was essentially reversed. In aether theory, we essentially have a precursor to a more sophisticated concept (spacetime). Scientific revolutions are not all equal, and so neither is the loss that results. In some cases, Kuhn losses can be recovered and contribute to the advancement of a specific theoretical framework. Midwinter and Janssen [7] introduce us to the physicist/chemist Van Vleck, who improved upon the Kuhn loss introduced when quantum theory was introduced and replaced its antecedent theory. Van Vleck did this by borrowing mathematical formalisms from the theory of susceptibilities, and bringing them over to physics. While neither a restoration nor a paradigm shift, Van Vleck was able to improve upon the ability of quantum theory to make experimental predictions.

Tongue-in-cheek description of an empirically verified of phlogiston theory. COURTESY: [8]

Now let us revisit the Kuhnian content of the ENCODE kerfuffle vis a vis this framework of positive/negative Kuhn loss and Kuhn recovery. Is this conceptual clash ultimately a chance for a gain in theoretical richness and conceptual improvement? Does the tension between computational and traditional views of biological function neccessitate Kuhn loss (positive or negative)? According to the standard dialectical view [9], the answer to the former would be yes. In such case, we might expect a paradigm shift that results in an improved version of the old framework (e.g. 'positive' Kuhn loss). But perhaps there is also a cultural mismatch at play here [10] that could be informative for all studies of Kuhn loss. Since these differing perspectives come from very different intellectual and methodological traditions, we could say that any Kuhn loss would be negative due to a mismatch. This is a bit different from the phlogiston example in that while both approaches come from a scientific view of the world, they use different sets of assumptions to arrive at a coherent framework. However, what is more likely is that computational approaches (as new as they are to the biological domain) will influse themselves with older theoretical frameworks, resembling more of Kuhnian recovery (the quantum/antecedent theory example) than a loss or gain.

It is this intellectual (and logical) reformulation that will mark the way forward in computational biology, using an integrative approach (as one might currently take for granted in biology) rather than reasoning through the biology and computation as parallel entities. While part of the current state of affairs involves a technology-heavy computation being used to solve theoretically-challenging biological problems, better logical integration of the theory behind computational analysis and the theory behind biological investigation might greatly improve both enterprises. This might lead to new subfields such a the computation of biology, in which computation would be more than a technical appendage. Similarly, such a synthetic subfield would view of biological phenomena much more richly, albeit with the same cultural biases as previous views of life. Most importantly, this does not take a revolution. It merely takes a logical reformulation, one that could be put into motion with the right model system.

[1] the word "paradigmatic", translated into binary. COURTESY: Ashbox Binary Translator.

[2] Kuhn, T.S.   The Structure of Scientific Revolutions. University of Chicago Press (1962).

[3] Hoyningen-Huene, P.   Reconstructing Scientific Revolutions. University of Chicago Press (1983).

[4] Doolittle, W.F.   Is junk DNA bunk? A critique of ENCODE. PNAS, 110(14), 5294-5300 (2013).

[5] The ENCODE Project Consortium   An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74 (2012).

[6] Vihalemm, R.   The Kuhn-loss Thesis and the Case of Phlogiston Theory. Science Studies, 13(1), 68 (2000).

[7] Midwinter, C. and Janssen, M.   Kuhn Losses Regained: Van Vleck from Spectra to Susceptibilities. arXiv, 1205.0179 [physics.hist-ph] (2012).

[8] DrKuha   The Phlogiston: Not Quite Vindicated. Spin One Half blog, May 19 (2009).

[9] what we should expect according to dialectical materialism: adherents of two ideologies struggle for dominance, with an eventual winner that is improved upon the both original ideologies. Not to be confused with the "argument to moderation".

[10] for more context (the difference between a scientific revolution and a scientific integration) please see: Alicea, B.   Does the concept of paradigm shift need a rethink? Synthetic Daisies blog, December 25 (2014).

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...