We are living in a fever dream

About a week delayed, however last Monday President Donald Trump, in a step toward establishing a ‘Space Force’ used a segregation-era phrase. In the unlikely event that this new, sixth branch of the U.S. military actually comes to fruition, the story of its founding will be etched in history using the same vocabulary that summarized Jim Crow legislation. While the idea of the existence of a galactic military may appeal to the my Sci-Fi nerd side – and ignoring its possible Non-Fi ramifications  –  this is hardly the illustrious and inspirational speech I would have hoped for. Life is weird sometimes.

 

trm

 

Reference:

Brice, Makini. “Trump Orders Creation of Space-Focused U.S. Military Branch.” Reuters, Thomson Reuters, 18 June 2018, http://www.reuters.com/article/us-space-moon/trump-orders-creation-of-space-focused-u-s-military-branch-idUSKBN1JE249.

Why ‘Failure’ Is Good For Science

Picture this. You’re grinding away at your lab bench or instrument workstation or computer (for those computational folks) for hours trying to come up with some usable data. You’ve spent the last few days trying new approaches to the same problem, to no avail. Maybe you’re sick with a cold. Maybe it’s late in the evening and you’re trying to get home. A notification pops up on your screen (we’re sticking with a digital scenario); you have your data – and, yet again, the experiment didn’t work or the results don’t make sense.

This scenario is universal in all fields of science. All scientists can recall a point where hope was fleeting or simply nonexistent. Similarly, all scientists struggle daily with troubleshooting their experiments and equipment to get them working in the first place.

Scientists, much of the time, bear the burden of these indelible realities of their craft in relative silence – only speaking of them in detail after their research has borne fruit. There is a lot at play that drives this.

First – Science is expensive. Expensive enough that most scientists are not funding their own research. Instead, they get their funding through grants from government agencies, non-governmental organizations (NGOs), and for-profit organizations. In situations where research funding is on the line, researchers are under pressure to perform. The result is that they may not be as forthright about the lack of exciting positive results as if the atmosphere was more conducive to such communication.

Second – Science is competitive. Whether we like it or not, the practice of science that produces positive results, in one field or another, comes with a certain degree of prestige or ‘bragging rights’, and while this competition can certainly give rise to innovation, it is not without its pitfalls. For example – Jonas Salk.

Jonas Salk has gone down in the annals of scientific and public health history as the man who developed the first functional AND safe polio vaccines. Salk obviously wasn’t the only person attempting to develop a vaccine, his rival Albert Sabin was also making great strides, thus he was pressured by the weight of the prestige that would come with the vaccine’s discovery. Whether or not that pressure made his work go faster or not, we’ll never know, but I’d certainly be interested to know how quickly a vaccine could have been developed if the rival researchers could have had an open discourse about their ‘failed’ trials. It’s likely that, between the two of them, many approaches to the problem were repeated.

 

 

So what exactly is the difference between a scientific failure and a negative result?

A scientific study is conducted the formation and exploration of a hypothesis. For example, let’s say that the hypothesis of a particular drug study is that Drug X has some effect in treating a specific disease. In carrying out the study, the researchers find that Drug X has no significant effect in treating said disease. Is this a failure?

Absolutely not. This is a negative result.

Just because the result may not have been the desired result, does not mean it is a failure as there is still useful information to be gleaned from the study. Perhaps the molecular structure of the drug was not what was needed for the treatment to be successful. Perhaps the molecular structure was fine, but the method of drug delivery was lacking – rendering a potentially successful drug useless. There are so many questions that need to be addressed when negative results occur. Making negative results widely available to fellow researchers, instead of working them out on one’s own, perhaps only asking a few people for help, could potentially expedite the research process.

What does actual failure in science look like? Look to the example of Andrew Wakefield publishing his fraudulent paper on the link between the MMR vaccination and incidence of autism in children in The Lancet. More here. The failure in this being the scientific malfeasance of manipulating data to obtain a desired result as well as the nondisclosure of conflicts of interest. Wakefield received funding to look for evidence on which arguments against the use of vaccines could be based.

Nonetheless, science is an endeavor whose nature is largely trial and error (or negative results… or malfunctioning instruments) and it can be disheartening. The best case scenario is that, ultimately, the constitution of the scientist becomes a bulwark, holding fast against negative results.

P.S.

Stuart Firestein did an excellent segment on the topic on NPR’s Science Friday.

St. Patty’s Post: Beerzymes (Alpha & Beta Amylase)

Happy St. Patrick’s Day!

EDIT: This was obviously supposed to post on March 17th

Personally, this is one of my favorite holidays. Cured meats, good beer, and stories of missionaries driving snakes (an obvious metaphor for Irish druidism) from Ireland – what more could you possibly want?

In the spirit of the holiday, I’m going to showcase two interesting enzymes (or beerzymes as I whimsically and somewhat superfluously call them) that are necessary for the fermentation process of brewing beer – α(alpha) and β(beta) amylase [AM-uh-lace].

First – what’s an enzyme? An enzyme is specialized molecule, or protein, that biological systems use to perform certain functions. For example, in the process wherein our cells divide, the DNA housed inside our nuclei must be replicated for use in the “new” cell. This process requires the action of a DNA helicase, which is an enzyme that partially unravels the DNA double helix such that the cell’s replicative machinery can get in and do its job.

Enzymes have many functions. The function of the class of enzymes known as amylases is to break down starch and glycogen, both of which are glucose polymers (molecules consisting of repeating units of glucose molecules), by hydrolyzing [HI-dro-LIZE] or “cutting” the chemical bonds that glucose polymers use to link glucose, the α1→4 glycosidic [GLY-co-SID-ick] bond.  The human body naturally produces amylases for all sorts of purposes such as when α-amylase is secreted from the salivary glands to aid in the breakdown of starchy foods like rice and potatoes. Fun fact: amylases were the first class of enzymes to be discovered via the work of Anselme Payen in the early 1800s.

2xfr b amylase.png
Structural representation of the enzyme beta-amylase from barley.1

So what do these enzymes do for beer?

Well, the first step in the production of is creating a mash, or a sort of “tea” using mashed grains and hot water. Mashing grains releases starches into the water, becoming a mixture called the ‘wort’. Typically, many of these sugars released, at the beginning of the process, are not fermentable, meaning, they cannot be digested by yeast to produce alcohol. In order for these sugars to be fermentable, they need to be broken down into smaller constituents, the monosaccharide glucose and the disaccharide maltose. Once this is done, the yeast that is added to the wort can begin digesting the sugars, starting the process of fermentation.

More information about carbohydrates here.
File:Starch-breakdown-sites.jpg
Diagram showing the action sites of alpha and beta amylasae on a starch molecule. Courtesy of Wikibooks user Lrh.

Not all amylases are the same, alpha and beta amylases perform similar but different jobs. Alpha amylases hydrolyze [HI-dro-LIZE] or “cut” glycosidic bonds in random areas along the glucose chain, eventually degrading the starch completely into individual glucose molecules. Beta amylases, however, can only hydrolyze every other glycosidic bond, forming maltose.

At the end of the mashing period, the wort contains (from the alpha-amylase) and maltose (from the beta-amylase), two principal sugars used in fermentation. The wort will also contain a considerable amount of glucose-1-phosphate, a phosphate-linked sugar that is a product of the alpha-amylase function. Yeast cannot internalize glucose-1-phosphate, thus those glucose molecules are non-fermentable. This means that beta-amylase largely produces the greatest amount of fermentable sugars.

Being that these two enzymes produce different, useful products, brew masters can manipulate their ratios of use their characteristics to their liking. The relative levels of the enzymes can be controlled by the temperature level of the mash as the two enzymes have differing optimal temperatures.

Alpha-amylase functions at temperatures between 145° to 158° F, while beta-amylase operates between 131° and 149° F.2 Therefore, if you want to increase the amount of easily fermentable sugars, increasing the amount of alcohol in the final product as the yeast are able to consume more, you would want to mash your grains at temperatures optimal for the function of beta-amylase. If you want to maintain some of the sweetness of the sugar in your brew, you would run past the beta-amylase’s optimal temperature and mash within alpha-amylase’s optimal temperature range.

References

  1. Rejzek, M.; Stevenson, C. E.; Southard, A. M.; Stanley, D.; Denyer, K.; Smith, A. M.; Naldrett, M. J.; Lawson, D. M.; Field, R. A. (2011). “Chemical genetics and cereal starch metabolism: Structural basis of the non-covalent and covalent inhibition of barley β-amylase”. Molecular BioSystems. 7 (3): 718–730.
  2. Parkes, S. (n.d.). Understanding Enzymes: Homebrew Science. Retrieved from http://byo.com/hops/item/1543-understanding-enzymes-homebrew-science