Wikipedia:Reference desk/Archives/Science/2020 April 8

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April 8

genotype vs genome

These two terms are similar, and describe the whole library of genes of a specific organizm. Still, they aren't synonyms, but, apparently, the respective articles here don't reflect the difference between the two, & I'll be glad to get a clear destinction between them. Thanks, בנצי (talk) 06:16, 8 April 2020 (UTC)

Your statement that they both "describe the whole library of genes of a specific organism" is not really correct. "Genotype" is generally only used for a single gene locus or a small subset of loci. A pea plant can have a homozygotic genotype for petal color, for example, but it is highly unlikely to be homozygotic throughout its entire genome. Basically, genotype is used for the particular portions of DNA that you are interested in in a particular experiment, genome is used for the totality.--Khajidha (talk) 12:08, 8 April 2020 (UTC)

Friction of interstellar medium

Suppose an interstellar spaceship is moving at some extremely high speed (possibly near light speed) in the outer space. Would the dispersed atoms of interstellar medium turn into some torrent of hot plasma at such speeds, similar to aerodynamic heating of supersonic jets? Thanks. 212.180.235.46 (talk) 09:40, 8 April 2020 (UTC)

We have Interstellar travel#Interstellar medium, which touches on the issue but is not particularly helpful beyond saying, "Yeah, there could be problems." -- ToE 15:49, 8 April 2020 (UTC)

Is it possible to calculate at what speeds the medium becomes a problem for a spaceship? I assume it would be very big numbers due to medium's very small density. 212.180.235.46 (talk) 16:08, 8 April 2020 (UTC)

That's a little difficult since a cutoff needs to be selected for when it is a "problem." Drag, to some extent, always exists in outer space since outer space is not a perfect vacuum. It is certainly possible to numerically calculate that amount of drag, but as for when it is a problem? Needs a cutoff. Also, it would differ based upon the shape of the craft in question, just as it does in our atmosphere, and the composition of the medium, which may not be uniform. --OuroborosCobra (talk) 18:50, 8 April 2020 (UTC)

I think that for speeds >0.1c this will be a big problem. Ruslik_Zero 17:30, 8 April 2020 (UTC)

A back-of-the envelope calculation suggests the same. It will be a huge problem well below the speeds where you have to take account of relativistic effects. At 0.01c, γ = 1.00005, which is still very close to 1. But assuming hydrogen gas (H₂) at a density of 10⁶ molecules per cm³, the kinetic energy of the impacting gas to be absorbed will be comparable to a vehicle travelling in air at Mach 2.5 to 3. For 0.1c, the equivalent becomes Mach 25 to 30, which is about today’s limit, not sustainable over extended periods.  --Lambiam 19:33, 8 April 2020 (UTC)

@Lambiam: The back of my envelope doesn't seem to match the back of yours. Mine estimates the ratio of the mass density of air to that of your cold interstellar medium to be about (2.7 ⋅ 10¹⁹ molecules per cm³ ⋅ 28.8 u per molecule) / (10⁶ molecules per cm³ ⋅ 2 u per molecule) ≈ 3.9 ⋅ 10¹⁴, whose cube root is roughly 73,000. And 0.01c / 73,000 ≈ 41 m/s. Am I doing something wrong? -- ToE 23:27, 8 April 2020 (UTC) (This assumes KE flux goes as v³ρ since we have v for the mass flux times v² for the KE per unit mass.)

I had a typo in the value for u in kg (I used the air density value of 1.2 kg per m³ from Atmosphere of Earth and therefore converted hydrogen mass to MKS). After correcting, for v = 0.01 c I get 42 m/s = Mach 0.123. To get the equivalent of Mach 25 you need to go up to v = 0.93 c, at which speed relativistic length contraction is quite significant. Caveat for future interstellar travellers: this assumes interstellar gas only; dust and oncoming traffic have been ignored.  --Lambiam 07:49, 9 April 2020 (UTC)

Does anyone know what sort of design or engineering would be needed to deal with this? "Lighthuggers" in Alastair Reynolds' Revelation Space series are streamlined for this reason. Would that help, or would the energies involve make streamlining irrelevant? Iapetus (talk) 08:42, 9 April 2020 (UTC)

My mental model is that of a steady state with a hot blanket of compressed plasma over the front of the moving object. Impacting gas is caught in the blanket (inelastic collusion); the steady state is maintained by the plasma flowing off in a laminar flow along the sides. This model is why I think the kinetic energy of the headwind is the relevant quantity. The easier the plasma can flow off, the more the internal pressure in the blanket will be reduced, and so the less it will heat up the object. Streamlining should ease the flow, but I don’t know how to do the modelling that will give me quantitative results.  --Lambiam 11:54, 9 April 2020 (UTC)

The average density of the interstellar medium is actually about 1 cm⁻³. However the problem is not ram pressure but radiation. At 0.1c each proton will hit the spacecraft with the energy of about 5 MeV, which is high enough to damage the wall and produce gamma radiation. Ruslik_Zero 19:54, 9 April 2020 (UTC)

Our article Interstellar medium states that in cool, dense regions, matter is primarily in molecular form, and reaches number densities of 10⁶ molecules per cm³. Is that wrong? You appear not to think that a steady-state plasma blanket will form that is dense enough to capture the protons before they hit the hull of the spacecraft. Or would its temperature also go up to 5 MeV, in which case it does not make a difference whether it's there or not?  --Lambiam 21:17, 9 April 2020 (UTC)

Such density is only reached in giant molecular clouds, which volume is negligible. On the other hand the density of Local Bubble is ~0.05 cm⁻³. On average it is 0.5–1 cm^-3. I am not sure why the plasma blanket should appear at all? The density is so low that the mean free path of particles is about 0.001 pc. Ruslik_Zero 20:34, 11 April 2020 (UTC)

Reworking the back-of-the envelope calculation above, but with 1 hydrogen ion per cm³ instead of 10⁶ molecules per cm³, changes the density by a factor of 2·10⁶ giving 7.8⋅10²⁰, whose cube root is roughly 9.2⋅10⁶. Thus the 0.5ρv³ KE flux equivalent of interstellar 0.01 c would be only 0.33 m/s at sea level, with that of 0.1 c being 3.3 m/s. -- ToE 16:20, 14 April 2020 (UTC)

But other effects scale considerable worse than cubic. Atmospheric entry#Reentry heating states that "radiative heating is proportional to the velocity exponentiated to the eighth power." (Here is a discussion on StackExchange prompted by a mention of the phenomenon by Elon Musk in the context of SpaceX Starship development.) So, *if* radiative heating scales as ρv⁸, and *if* this holds across a wide ranges of magnitude, then we could make a comparison.

In 2006, the Sample Return Capsule of NASA's Stardust comet probe reentered the Earth's atmosphere at 12.9 km/s, the fastest reentry speed into Earth's atmosphere ever achieved by a human-made object. Peak reentry heating occurred at an altitude of 61 km, (200,000 ft)^[1], where the atmospheric density is 2.73·10^-7g/cm^3[2], a factor of 1.65·10¹⁷ greater than that of the 1 hydrogen ion per cm³ interstellar medium. The eighth root of that is 142, multiplied by 12.9 km/s^* gives 1830 km/s = 0.006 c. -- ToE 16:27, 14 April 2020 (UTC) * Peak deceleration for Stardust's SRC occurred at 55 km, after peak heating. Still, peak heating should have happened at a velocity somewhat below 12.9 km/s, but I couldn't find its deceleration profile, so these numbers should be good enough for a rough comparison.

What makes a complex compound react with another complex molecule, but not with simple ones?

I read about Diisopropyl fluorophosphate and I see it reacts with very limited number of molecules (especially enzymes) but with simple molecules (for example sugars) it does not. Which leads me to the question: What makes a complex compound (such as DF) react with another complex molecule, but not with simple ones?--Exx8 (talk) 10:54, 8 April 2020 (UTC)

That's a HUGE question, and it really requires one to dig deep into some rather complex ways chemistry works in general. The best I can say is that, when looking at how a substance will interact with our biology, there are two main factors to consider: pharmacodynamics and pharmacokinetics, which aligns well with the two aspects of how a chemical reaction progress is measured: Thermodynamic versus kinetic reaction control. Thermodynamics (for our purposes for answering this question) deals with the beginning and end state of a particular reaction: That is, what are the starting materials, what are the end materials, and the total amount of energy change necessary to get us from the start to the end. Kinetics deals with the middle bit: What are the reactants doing between the start and the end to make that happen. That brings up all sorts of issues like reaction mechanism (the steps that have to occur) and reaction rate (how fast those steps occur). You can have a reaction that is thermodynamically favorable (which means that, for example, it is highly exothermic, it releases LOTS of energy) but which is kinetically very unfavorable (that is, it takes a stupidly long time to release that energy, like decades or centuries). Think about something simple like rusting: The act of oxygen combining with iron to form rust is HUGELY exothermic, about -826kJ/mol, which means that (doing a quick calculation) about 100 grams of iron, in the course of rusting, would release enough energy to raise 1 liter of water's temperature about 200ish degrees celsius. However, rust happens so slowly (over the course of years or decades) that that energy comes out in such a small trickle, we don't notice it. The same is true of reactions in our body; and I suspect that's what is going on here. The DF may be able to react with any hydroxy group from a thermodynamic perspective but the kinetics are only favorable under very specific conditions. --Jayron32 13:46, 8 April 2020 (UTC)

Another idea to consider is that molecules aren't just nebulous "things", but instead are actual 3D things, composed of actual atoms that have actual positions in the molecular structure. A large molecule is composed of lots more pieces than a simple one, and those different regions might be quite different from each other (rather than multiple copies of same/similar pieces), increasing the overall "complexity" of it. If two complex molecules each have a piece that can react with each other, then "the complex molecules can react with each other" regardless of all the other pieces each has. So there are possibly many more ways a complex molecule can react, because it has a greater diversity of parts that might just happen to match some other molecule's part. A simple molecule doesn't have as many options.

A second idea is that in a complex molecule, several different pieces can operate together, where one increases or decreases the reactivity of another. So a large enzyme might be specific for a certain target molecule because one part of the enzyme prevents other (non-target) molecules from getting close to the part of the enzyme that reacts. Or one part could supply an additional atom (or provide an anchor to hold an atom) to make the reaction easier. Diisopropyl fluorophosphate has fairly large groups surrounding the phosphorus atom and the oxygens of glucose are each close to the large parent structure. So it is difficult for those two pieces to get together. Perhaps they would react if they could get together? That's Jayron32's discussion of being thermodynamically favored but kinetically slow. The oxygen of serine (part of the enzyme that reacts with DFP) is further from the complex parent (it goes HO-CH2-[big] rather than HO-[big]). And the other parts of the enzyme near the serine appear to enhance the reactivity or hold other specific atoms in the proper place for the reaction to occur efficiently. DMacks (talk) 14:04, 8 April 2020 (UTC)

They have to "fit" in a very real physical sense. A key may open a complex lock but be useless for a much simpler lock.  --Lambiam 19:36, 8 April 2020 (UTC)

Yes, see lock-and-key model. One aspect of the question that I seem to pick up on is an implication that enzyme inhibitors, etc. react with "the whole enzyme". Actually, in most reactions catalyzed by enzymes, the only part of the enzyme that actually participates in the chemical reaction is the active site, which is usually just a few amino acid molecules. (Restating here more briefly some of what DMacks said above.) This is the case with DF inhibiting acetylcholinesterase: DF binds irreversibly to its active site, preventing it from binding acetylcholine. The rest of an enzyme serves various functions, including bringing the components of the active site together in 3D space, orienting substrates and cofactors, regulatory functions, and more. Dive into enzyme to start learning more. There's a lot there; someone can easily pursue a whole biology career just focusing on enzymes. --47.146.63.87 (talk) 22:46, 8 April 2020 (UTC)

Catalytic triad is a great example of the cooperation of a few specific parts of an enzyme to accomplish a certain reaction. DMacks (talk) 03:02, 9 April 2020 (UTC)

Your question a little misleading with your example. Your example is not a particularly big molecule. More like a middle molecule. But yes, the =O and -F are gonna be the more reactive parts, than the -CH3. I think the ultimate answer goes to electrical charges. For example, a compound like hexane, /\/\/\ won't react with other hexane to form \/\/\/\/\/\/. You have to heat or destroy an edge to get a charge that will combine or react with others. For example, \/\/\(+) and \/\/\(-) will therefore react or combine. Note that my answer is for real beginners, someone can advance on it. 67.175.224.138 (talk) 15:18, 9 April 2020 (UTC).