Monday October 14, 2013

This is Nature October 10 2013, Vol. 502, Iss. 7470, Pp. 141-264.

1. Big weapons have little downside.
2. Secrets of trial data revealed.
3. Earth science: The timing of climate change.
4. Quantum physics: Watching the wavefunction collapse – – I’m not reviewing this article (but bookmarked) because I simply do not have a strong enough foundation in QM.
5. Cell biology: Molecular clearance at the cell’s antenna.
6. Microbiology: RNAs at a fever pitch.

1. Big weapons have little downside

Context: Does forming mating-associated extreme body-parts challenge survival, since that would prove their vitality (cf. mating rituals)?

Result: There is no correlation between male rhinoceros beetles’ horn size and obvious survival factors (e.g. general survival, flying, immune function, etc).

Implications: First of all

1. the researchers say that “weapons may evolve along with traits that let males make the best use of them, offsetting survival costs”, about which I note that
2. these weapons may not be paradigmatic of other extremes (e.g. peacock tails). But I would also say that
3. this allows for the possibility that such “extremes” evolve within a survival/phenotype landscape which is already de facto such that it may be explored, viz. via evolution. I point out what the researchers’ point out; there is an incredible amount of variation of horn shapes amongst beetles.
4. Does this mean that evolution does not explore completely blindly? The answer can be, “No, it is completely blind,” since a description of the variation amongst horns amongst species, occurs after the fact, and does not necessitate it. By contrast, the answer, “Yes, there is a sense of phenotypic landscaping,” can be imagined – what is harder is to imagine what is doing the imagining!

This imagining follows a preceding question, “If yes, how is that possible? Doesn’t sensing a phenotype/survival landscape require sensing (even if virtual) of the future?” My answer comes about by realizing that this mode of phenotypic flexibility can manifest itself by flexibility to noise (as a side-note, I note that this rule relating to survival/phenotype can be described in the parallel relationship between genotype/phenotype, etc).

In other words, “Metaphorically, evolution predicts the survival/phenotype landscape of its members by experiencing their adaptability to any noise along this landscape. Whether or not this noise is the result of whatever sort of variation between phenotype and survival function, it implies a scope within which a definite phenotype (i.e. low noise) phenotype can be altered whilst achieving the same phenotype. Of-course that scope can also be used to explore improved survivability, and that could (metaphorically) allow for motivation for especially exploring that landscape.”

Note that the above answer rides a tentative and pseudo “Yes” to the question of, “Does sensing a survival landscape require sensing the future?” It is a “pseudo-yes”, since the answer reframes the expectations of “sensing the future.” But by being a “pseudo-yes” it is also a “pseudo-no”; this follows from a need to reframe “sensing the future” but also reframe (by metaphors) a model of an evolution that senses. Thus, “No,” it does not require future-sensing per se, but, “Yes,” it involves a phenomenon that is a metaphor of future-sensing.

I can expand on this understanding of noise. It’s like a phenoset (as a species’ ecosystem is to an individual’s habitat, a phenoset is to a phenotype). It’s like noise is the range of meanings that a formal system can generate. This does not negate the “noisiness” of this definition, and a particular individual can reside in a less optimal frame (i.e. imperfection still occurs since the noise is not truly homogenous). [Enough said (cf. completeness) on this matter].

2. Secrets of trial data revealed

This News piece concerns the data that is hidden when companies conduct trials, (esp. negative data that reduces the apparent utility of an ostensible product). Specifically, it looks at information, including rates of side-effects, that is present in private CSRs but not in the published literature.

“According to the analysis, crucial trial information, such as mortality rates and serious side effects, is missing from much-published data. But it can frequently be found in standard non-public documents prepared by industry, known as clinical study reports (CSRs). Missing information uncovered by the study includes details of depression symptoms in trials for antidepressant drugs and details of heart attacks and strokes in diabetes-drug trials.”

3. Earth science: The timing of climate change

This article refers to an article in the current journal. Amongst the achievements there, are, ” two refreshing advances to our understanding of climate change. First, it concentrates on climate variability instead of overall mean change. Second, it identifies the year in which climate change will cross the threshold whereby events that are currently regarded as extreme become the norm.” The latter will be, “when continuous deviation from mean climatic conditions that have prevailed over the past century and a half is likely to occur”

1. Measure climate variability instead of mean change.
2. Define the date by which current “extreme climate” become “within climate normal range”.
3. This “departure” will occur at the tropics first and at the poles last.
4. Thus tropic biodiversity expected to be hit first.

4. Cell biology: Molecular clearance at the cell’s antenna

This opens up a field of MCB I didn’t know. For starters the significance of the primary cilium in eukaryotes, including their potential role in sensing their environment for the cell.

In any case, these studies referred to in this publication study the linkage that associates autophagy with these primary cillium.

5. Microbiology: RNAs at fever pitch

Result: A particular bacterium resists the immune system by sensing the host’s temperature. It does so, (and this is the punchline) by sensing the temperature via a mechanism involving a change of state in RNA. At higher temperatures a structure (e.g. hairpin) in the RNA is dissolved, allowing access to translation machinery (e.g. ribosomes), which translate the relevant proteins (i.e. in this case for surviving an immunological attack). Thus there is (in effect) an RNA thermosensor.

Of interest: First, it is a role for RNA (cf. mRNA, siRNA, RNAzymes, etc). See also “riboswitches” in the quote below.

Interesting quote: “The discovery of three RNA thermosensors raises the question of how prevalent such sensors are in nature. By far the most common genes known to be controlled by RNA thermosensors are those that encode heat-shock and virulence proteins. Recently, however, an adenine-sensing riboswitch was found to be markedly temperature responsive. Riboswitches are metabolite-binding RNA elements that control numerous metabolic pathways. They are commonly believed to exist in two alternative conformations, either with or without their ligand. The adenine-binding riboswitch of the human pathogen Vibrio vulfnificus, however, adopts three distinct states, and the ambient temperature shifts the equilibrium between two ligand-empty states that have either low or high ligand affinity”.

Thus this reveals the sufficiency of RNA for basic life… that’s probably the main theory that interested me to read this article, viz. I now have a more elaborate perspective on what RNA is, and what how its details can contribute to a MCB paradigm of a living system.

But regarding individual details, I can wonder how unique they are, and when are they also examples of categories. For instance, is thermosensing one of many sensory mechanisms affected by RNA, and within each of those modes, what is the extent of information synthesis (e.g. differentiating a temperature range versus just a “greater than” point, as studied here).