Does it behoove better lingo?

Just like the good sommelier delights us with their expansive full-bodied descriptions of wines, connoisseur molecular and evolutionary biologist have their own lavish use of terms.

We don't deal with time, we deal with "evolutionary time", cause those bacteria in our -80C stocks are certainly having some non-evolutionary time out.

We don't say we've detailed the properties or characteristics of something, we instead say we've "characterized" it.

We would not only say we did the bench work on something, you will also hear about doing the "wet lab" on this or that.

We don't rebuild or reconstruct things, we "refactor" things.

We wouldn't refer to chromosomal positions or locations, rather we would talk about chromosomal "loci".

Instead of asking "what's being detected", we prefer to ask "what's the readout?".

We like to refer to "trans acting" as something caused by other locations in the genome or elsewhere, whereas "cis acting" generally means from the same DNA sequence or in the same place.

We don't merely plan ahead, we do "forward planning".

We can wonderfully bundle all our data analysis methods such as genomics, proteomics, metabolomics, transcriptomics, systems biology, bioinformatics, etc., as "-omics" or often referred to as multi-omics.

We don't just say isolated clones or isolates, we may say "single-cell derived clones".

You may see some data set or plot with lots of variability, but we see it's "noisy". Simply put, anything away from average is noise. Moreover, when given essentially equal conditions, deviations from average are just natural noise.

Most often we want to avoid non-specific and "off-target" effects. If something is "non-specific", it'll indiscriminately interact with multiple things. If it has off-targeting, it could create havoc elsewhere and much less efficient.

We may avoid the word detrimental and instead say "deleterious", so for example purifying selection removes deleterious mutations from the gene pool.

We don't either say "complete" as in "complete review", we definitely prefer "comprehensive".

And we say "isogenic" when a population of organisms is the same genetically or has the same genetic constitution...same genotype...same genetic makeup.

We certainly prefer how the word "empirical" sounds when we want to refer to experimental evidence or observations.

We do not test "in a computer", we test "in silico".

We don't say something increased to 10-times more, but rather say it increased "an order of magnitude" or that it had a 10-fold increase.

We just love acronyms, so get used to it. "Genetic engineering" made possible the creation of GMOs (genetically modified organisms) and more recently "synthetic biology" is bringing us a myriad of SBOs (synthetic biological organisms). To clarify, "genetic engineering" and "synthetic biology" are considered different fields, where the first refers to single gene transfers (genetic modifications usually performed on crops) and the later refers to the design of more complex genetic devices (usually in bacteria or yeast) that perform tasks not generally found in nature, which in some instances involves the use of genetic sequences that have never been seen in nature.

We do not improve the production or "yield", we get higher "throughput". Thus, we like to use and develop "high throughput" technologies, and it's just another way of saying high efficiency, but specifically by allowing to rapidly produce results while dealing with very large scale data sets. A general approach to achieve high throughput is by automating processes or experiments to allow large scale repetition.

We like to segregate or partition, instead of just separate something, e.g., we talk about "segregational stability" of plasmids to refer to how they distribute/separate during bacterial replication.

We don't produce a "collection" of cells, DNA, proteins, antibodies, genes, clones, etc., we produce "a library" of these.

We do not "separate" things, we "fractionate" them.

As scientists in general, we may want to refer to a process or description as "high-level" or "low-level", though it's highly subjective, it is commonly used by paper reviewers, i.e., "the high-level purpose is not clearly stated" or "a tedious low-level description".

We scientists like to talk about the "efflux" of something, which is nothing but a fancy word for out/output or the outward movement of some substance.

As we develop a technique/system/device and achieve a 1st working prototype, we like to say we have the "first-generation" tool or process. Think about it, the "second-generation" will give us material for a second paper/publication!

We may go beyond simply saying that a mutation is neutral and specify that it evolved by "genetic drift"...cause even random chance is never as simple as it seems.

We do not say something is the "same", we like to say something is "conserved", cause in terms of evolution good/useful things remain the same, particularly across species.

When comparing genomes that have genes located at similar positions, we don't just say their genes are organized similarly, we'll say there's "synteny", which is the organizational similarity of genome components, that is, it is the conserved order of blocks of sequences between chromosomes compared with each other.

We don't just use an approach, we use a "systematic approach", meaning it is methodical, planed and executed step-by-step. We don't just sift through our data, we systematically sift through our data! Think of it, we really wouldn't want people to think our approach is some random undertaking! So next time, instead of simply saying you'll delete genes one-by-one, you will rather say they'll be systematically deleted.

We don't look at some "part", we say we look at the "moiety" or a specific "constituent".

We do not study things in their "environment", we study them in their "milieu"...sounds more elegant doesn't it?

We may say that promoters "drive" gene expression or a given gene, instead of saying they regulate transcription.

We talk about "leaky" gene expression, to mean it isn't in a complete OFF state, but that it continues to be expressed at very low levels. Not very fancy, but very convenient term.

We don't deal with "supposed" or "apparent" (generally considered as) things, rather "putative" stuff. So if something has been proposed or it isn't yet an accepted fact, then it's just putative, such as a putative pathway.

For us, things don't just get filtered out due to restricted/limited selection processes, they go through "bottlenecks". In fact, without extreme "bottlenecking" we wouldn't be able to neatly measure spontaneous mutation rates minimizing effects of biased selective forces.

For us, things aren't just in stand-by, in some wait list or under development, our ongoing projects and products are in our "pipeline".

Very similarly, we may derive something "Prima facie", that is, our understanding from just a first impression, and what is to be taken as correct until proved otherwise.

We won't just say we do genome analyses, we do "functional genome analyses", because it sounds more serious!

We don't just say things are unchanging, we prefer saying they are in "steady state". So we may talk about genes turning from an OFF steady state to an ON steady state...just because it sounds cute and technical.

We prefer the most simple explanation, but we say it is the most "parsimonious". Technically, it means the simplest evolutionary path to explain how something evolved/branched into its current form.

We wouldn't say something was built from scratch or "newly" made, we like to say it was built "de novo" or it's a de novo approach and so on.

We don't just say something has "unknown or inactive function", we will say it is "cryptic", (i.e., cryptic plasmid, cryptic enzyme, etc.). Thus, we call something cryptic when the function is either unknown or not always present or expressed. One of the best examples of something cryptic is a once functional gene that has been damaged due to mutations.

When something is "caused by" or "facilitated by" something else, we like to say "mediated", particularly if it was made possible by that something else.

We talk about "bottom-up" and "top-down" approaches, the first meaning an approach that builds things from scratch starting from the most simple parts and the latter is an approach that takes what's already there and cuts it down to something simpler. In essence, bottom-up is constructive and top-down is deconstructive, both strategies are employed to study and understand the enormous complexity of biology.

We do not usually say "before" or "after",we prefer "upstream" or "downstream".

We do not use "a representative value" for something, but a "proxy" for it. That is, instead of saying that something is representative or indicative of something else, we'd say it is a "proxy" for it, i.e., size of phage plaques is a proxy for phage fitness.

We use the term "read-through" when something has passed a signal without the expected response to it, such as transcriptional or translational readthrough, where a transcription terminator or stop codon are not recognized (e.g., when a polymerase overrides termination) or have mutated to lose their function.

As you gather data from experimental methods, tools, instruments or programs, we will not ask what are the results, but instead what's the "readout".

We do not briefly expose cells to a "dose" or an "amount" of some radioactive compound, these are briefly exposed to a "pulse" of the specific radioactive compound.

We don't even say something is not needed, we say it is "dispensable", i.e, the S1 protein is dispensable for translation of leaderless mRNA!

We don't just find causal agents, but "determinants", e.g., pathogenic "recognition determinants" or "virulence determinants" are of much interest for molecular biologists.

We may not just add some extra layers (multi-layers!) of protection or benefits, you may hear us talking about "higher-order combinations", such as in "higher-order combinations of biocontainment safeguards".

We don't develop things that affect/generate many things at the same time, we do things that do "multiplexing".

When two biomolecules typically interact or react with each other (e.g., enzyme-substrate or ligand-receptor pairs), we say one is the "cognate" of the other. We may just use the term cognate to mean "genetically similar" or more generally to refer to any two things that are related or connected to each other in some way. For example, you may read about some biochemical machinery and its cognate host strain.

We don't merely say something is near or distant, we rather say "proximal" or "distal". For example, we aim to identify proximal and distal gene regulatory elements.

When we look at gene expression, often we do so by comparing expression to some genes that are used by the cell for its main functions, and these very stable genes we call "housekeeping genes". The advantage of determining gene expression relative to housekeeping genes is that these are stable under several different conditions and thus multiple genes can be compared simultaneously.

We do not say that a component's function can be by carried out by another thing, or that the same function is performed by a different components,we simply say it is "redundant".

We like to say something is "degenerate" if it has the same function (under certain conditions) of another thing that has different structure or composition. Thus, you will learn that the genetic code is "degenerate", due to the fact that different codons (three letter nucleotide code that specify amino acids in a protein) can code for the same amino acid. You may also hear about degenerate base pairing, for example as can be achieved with low annealing temperatures during a PCR. And that my folks is degeneracy!

We might eloquently state that a graph has a nice "hill coefficient curve", instead of simply saying that it shows a nice curve.

We may find that things "queue" up to be sequenced, more simply stated, things are awaiting their turn to be sequenced.

When something had high activity, catalyses multiple reactions at a time or makes many copies it is said it is very "processive". For example, the processivity of a polymerase enzyme is the average of nucleotides that it is able to incorporate before dropping off from the template strand. Processivity is therefore the enzymes ability to catalyze consecutive reactions without releasing its substrate.

We know for a fact that gene expression is in constant change, but we rather say a gene is in constant "flux" due to various processes.

We talk about something having a "basal level" in the cell, which would be an amount that will always be present, whether induced or uninduced. For example, we may talk about some basal gene expression, as the minimal amount of gene expression that's vital or essential for the organism to remain alive.

We do not say a gene is expressed continuously, we like to say it is "constitutively" expressed.

It's better if your experiments gather "longitudinal" data, that is, taking measurements at various time points throughout the duration of the experiment. An author didn’t feel he had enough fancy wording, thus he stated we could overcome knowledge gaps through “granular longitudinal studies”.

We may substitute the word "surrounding" for the word "satellite". For example, we have the term "satellite DNA", used to refer to tandemly (side by side...yes, tandem is another frequent molecular biology term) repeating, non-coding DNA, which happens to be the main component of functional centromeres, and form the main structural constituent of heterochromatin. Whoa! That's a mouthful! Anyway, these DNA sequences are called satellite because the nucleotide repetition numbers (frequency) vary such that when genomic DNA is separated on a density gradient, they form second or 'satellite' (surrounding) bands. Also, have you ever heard of satellite colonies? Well, those are smaller colonies that surround a larger colony. Usually the large one is resistant to an antibiotic and its secreting enzymes that degrades the antibiotic around it, thus allowing non-resistant colonies to manage to grow around/near it.

We don't just want to create genetic circuits, we'd like to have genetic "homeostatic circuits", which are expected exhibit balanced gene expression between two cell types. (Term used frequently by Andy Ellington)

We don't refer to existent organisms, molecules or any other currently present factors, but rather we refer to "extant" ones.

We don't make hypothesis to explain complications or mysteries, but to explain "conundrums".

You may hear some molecular biologist use the term "titration", which is actually a common technique to find out the concentration of a substance, as a kind of substitute for the word "sequester". Thus it's not uncommon to hear about the titration of some molecule A by molecule B, or to hear about some gene product "titrated out" by some other molecule.

We will avoid assuming something without any evidence at all, but we may politely say we "surmised" it (something...whatever came to our heads) because we felt we had the best explanation, although untested, but using it as a great excuse to not analyze it further!

Our results don't merely agree with other's results, they are "consistent" with them. Moreover, we usually don't prove anything (e.g., prove a hypothesis correct), but can show data that is certainly "consistent" with it. There's always that chance that you can obtain the exact opposite of your expected result, yet the truth would reveal itself if you replicate the experiment several more times.

If something seems to bind or react with everything, we like to say its "non-specific" or...better yet..."promiscuous". But we also talk about promiscuous plasmids, which can be conjugated/transformed into just about anything.

To say something happened "prior" to something else or that we have knowledge of it "beforehand" is almost profane. We'd rather say that it happened "a priori" or that we have a priori knowledge it. For example, some method may or may not rest on a priori knowledge of the elements under study.

We don't say "on site" nor "on the same place", we rather say "in situ" when we refer to something taking place in the same location where everything else is happening.

Instead of saying that a certain condition is not conducive to the growth of something, we'd say these conditions are "non-permissive". Thus, we like to make clear distinction between permissive (with special needs covered) and non-permissive conditions (lacking essential components for growh). So, we like to talk about non-permissive media and permissive media for biocontainment purposes.

More technically, we don't say that some cells may have "nutrient dependencies", we call those "auxotrophies". These auxotrophs will require external supplementation of some nutrient to survive because they lack the capability to manufacture it themselves.

In biology, "orthogonality" is synonymous with independently. If it's orthogonal, it may be varied independently without affecting the performance of the other components in a cell. Orthogonality is one of those big goals for synthetic biologists, but it's difficult to achieve in biology. It is the prerequisite for modularity (when components may be separated and recombined) and dividing a system into small parts that can be developed, optimized and developed independently. So, when we engineer a cell to express something distinctly from what's naturally occurring, we don't say it was expressed independently nor in parallel, we rather say "orthogonally". That's also why when something works across species, we say it's orthogonal. Some may go even further and express about some gene's/vector's/circuit's orthogonality as "host-agnostic" to simply mean that it will work regardless of the host it is used on.

Here's a big one: homology! Things are homologous when they are similar and we like to be very specific when we talk about the homology of genes or DNA sequences. So, when that homology is between different species (or bacterial strains), we call them "orthologous" genes (mostly considered homology after speciation), and when it's homology between different genes in the same genome or organism, these are "paralogous" genes (such as those resulting from duplications). We like if it works orthogonally, that is, if we can use something across species.

We might not want to say something, but instead "articulate" it.

We don't infect with two or more bacteria, we co-infect (thanks microbiologists!)

Since synthetic biologist like to put together biological parts arranged in very creative ways to do something different than their original function in nature, they may like to say they "co-opt" this or that to do something, e.g., genes get co-opted (adopted/borrowed) by other organisms. That is, the genetic sequences and the synthetic systems they build, which they refer to as "genetic devices", have been co-opted to do things like programming a bacteria to kill cancer cells, detecting some toxic chemical, etc.

We don't say that something is in its natural host...we rather say it's "indigenous".

We don't say that something might have effects on nearby things, but rather say it has "polar effects".

Sometimes we fault by adding some patchy explanation or makeshift solution, but we call them "ad hoc" elaborations. Worst science is when the scientist supports his theory with "ad hoc hypotheses", i.e. unsupported adjustments. We also say "post hoc", which would be explanations that came about after initial conceptualization.

We also prefer using the elegance of the word "contingency" instead of it's more simple counterpart "possibility" and avoid just simply saying that it depends on something. So, we have "contingent genes", genes which only express under certain conditions. We also talk about "contingency mutations", which are a kind of DNA modifications that can be restored and thus can switch genes between ON and OFF. This process is generally random but may be modulated by environmental conditions (also known as phase variation, which are either revertible or transient site-specific DNA rearrangements, like inversions, or modifications that do not alter the DNA sequence, like DNA methylation). Simply said, if it is "contingent upon" something, it basically means it depends on that. Given that something contingent may happen "only if" some requirements are met, evolutionary biologist love to study the role of "historical contingency" in evolution, that is, how past events shape an evolutionary outcome. In essence, if something is historically contingent, it is non-repeatable, due to the effect large and small historical variances have on the outcome.

We talk about heterologous expression, meaning, "the expression of a gene or part of a gene in a host organism, which does not naturally have this gene or gene fragment" (Wikipedia), instead of talking about expressing foreign genes. Something very common is to check if some gene works/behaves equally in another context, and so we clone it into a plasmid and transform it into another host, then if it works, we can say it is active both in heterologous contexts and within a natural host.

And, when we talk about genes expressed in a cell, but not from its genome, we say these are part of its "episome", e.g., plasmids, phages and transposons.

We don't merely refer to groups or collections with associations, we like to call them "consortia".

The united, collective or simultaneous emergence of things we usually refer to as "coherent".

Many molecular biologist, but in particular evolutionary biologists have a more fancy way to say adaptation, they may say the term "exaptation", because in many cases, instead of the organism making "de novo" adaptations, they tend to evolve by borrowing (or as we've mentioned before, "co-opt") something that initially had a different use and have it perform a new function that leads to the adaptation.

Instead of saying that some process increases the abundance of something, we say that it "enriches" it. So, something can be be highly enriched and that can be very convenient or interesting.

We don't simply do book keeping to make sure our samples are properly labeled, annotated or maintained according to experimental results....we "curate" our samples.

-- Main.GabrielSuarez - 10 Dec 2016

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Topic revision: r5 - 12 Sep 2018 - 14:54:21 - Main.GabrielSuarez
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