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What is limiting the accuracy of genome sequencing today?
What are the current limiting factors of genome sequencing accuracy? By accuracy I mean a closeness relation between the sequenced genome and the finally assembled (I am not sure whether there is a proper name for this metric). I hope this way of measuring accuracy is useful since it also captures errors introduced during read-alignment (if short-read sequencing technology is used) and assembly.
As I understand it, there are two sources of errors limiting accuracy: errors in determining the correct bases and errors made in data analysis (read alignment, assembly, etc.). Which of these two sources is responsible for most errors in long- and short-read sequencing techniques? Are a significant amount of errors stemming from the data analysis?
As @David guessed correctly, I am a student (engineering) and wondering whether accuracy may be significantly improved by better algorithms.
As I currently understand it, short-read sequencing techniques are accurate but the repetitive regions are hard/impossible to align, while long-read sequencing techniques are more error-prone, and long-read & accurate sequencing (HiFi) is very expensive. Hence, my overly simplified perspective suggests that algorithmic improvements may continue to improve cheap long-read accuracy through hybrid approaches or improve the alignment and assembly of short reads. Is that correct?
The resources I used were:
https://www.pacb.com/blog/understanding-accuracy-in-dna-sequencing/
https://spectrum.ieee.org/tech-talk/biomedical/diagnostics/99-9-percent-accurate-genome-sequencing
and the paper recommended by @Maximilian Press

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. In addition, there is more than one method for doing genome sequencing and they have different limitations — this makes your question as currently written too broad. Under researched questions may be subject to down-voting and closure.

I notice that you have not completed the [Tour]. Doing so will help you understand how this SE works. The help on asking questions is a good follow up. More specifically, it is helpful to provide context and support for any assumptions in San question. What makes you think accuracy is a major problem? And the idea that it has to do with algorithms suggests that you have not researched the topic, but are data scientist or programmer looking for a problem. Are you?

On reflection, I wonder whether you mean "accuracy" or something else. "Accuracy" of genome sequencing relates to correct identification of a bases at a particular position: how frequently will a sequence contain a G (say) where there is really an A. However that is not a major problem in sequencing eukaryotic genomes, especially those of higher organisms. The main problems are closing gaps representing regions that contain long stretches of numerous, repeated gene copies, and mapping stretches of near-identical DNA called segmental duplications. This is not accuracy, but may be what you meant

One that isn't on your list: cost.

In the form of Oxford Nanopore data, we have extremely long reads of low accuracy. These are not too expensive but on their own they are probably not viable for many applications.
In the form of Illumina data, we have extremely abundant, cheap, high-accuracy short reads, suitable for "counting" approaches. This is great for some variant calling approaches, and also for some kinds of orthogonal measures. On their own, they are not viable for a lot of applications, though.
In the form of PacBio (specifically HiFi) data, we have long(ish) reads of high accuracy. These are the total package, and you can in principle use them pretty much on their own for any given application that I can imagine. The issue is that they remain quite expensive.

Here is a recent review as a reference that goes over these (I haven't looked at it in detail, but it seems to capture the tradeoffs accurately).
We have gotten extremely good algorithmically at using all of these various kinds of data, and at hacking them in various ways to complement each other, but we can't get around the fundamental constraints of contiguity (length) and accuracy.
The HiFiAsm assembler for example is at peak performance for the moment, and it combines PacBio HiFi data with e.g. Hi-C data (a hack of Illumina) to deliver pretty much whole diploid human genomes, which is really an astonishing technical achievement. It was also used to assemble the redwood genome, which is 10X the size of the human genome.
The issue is taking these technical possibilities and getting them to a scale and a technological refinement where we can generate this extremely high-quality data at-will and for all of the applications where we would like to use it.

Do you really accept the poster’s assumption that accuracy is a major problem? Massive over-sequencing seems to deal with it.

@David I do in certain narrow contexts. For genome assembly, an application that the OP brought up, inaccuracy (and relatedly, incompleteness) is a major issue in the final product. One could argue both sides about whether accuracy at the read-level base call is particularly an issue. It is one that is now being addressed by technology in the fashions that you and I mention, but "massive oversequencing" is prohibitively expensive with the technologies that actually address the relevant problems.

@David Massive over-sequencing also only helps with sequencing applications where you have sufficiently large and pure amounts of source material. There are many applications where this is not the case.


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How do peroxisomes work?
I have this question from my book:
A child is diagnosed with an enzyme deficiency that prevents the production of hydrogen peroxide. What would the likely outcome be of such deficiency?
H2O2 is crucial to the function of peroxisomes and if h2o2 can’t be produced, peroxisomes can’t carry out their function. The functions of peroxisomes are:

lipid synthesis
role in pentose phosphate pathway
breakdown (digestion) of fatty acid chains

I would think all of these would be effected but according to the answer key, the only one that is considered is fatty acids. The logic is that fatty acids would build up and eventually apoptosis occurs. So my question is this, is h2o2 only necessary for peroxisomes to break down fatty acids and not synthesize lipids nor is it involved in the pentose phosphate pathway?
If that’s not the case, would I be able to know what would happen if the cell stops synthesizing lipids and how would the functional absence of peroxisomes impact the pentose phosphate pathway?

Welcome to SE Biology. We expect you to do some research as well as apply logic before posting here. There are two things you might check out. 1. Which of the three processes you mention require hydrogen peroxide? (Hint: two do not). 2. Which of the three processes only occur in peroxisomes?

I did do research but I’m still confused. I know peroxisomes’ primary function is breaking down fatty acid chains. I’m still unclear about the role of hydrogen peroxide. All I see is that the peroxides are have a part in the pentose phosphate pathway and lipid synthesis but don’t understand how they are involved. I thought given the name peroxisome, it is crucial for the peroxisome to function, but that doesn’t seem to be the case

OK. The pentose phosphate pathway does not involve hydrogen peroxide directly and occurs mainly in the cytoplasm. I gather it may have an indirect effect via the balance of oxidized and reduced NADP. An answer to your question would consider the actual chemistry involved. If nobody else does I’ll try to (but I’m still trying to find time to work on another question).

Thanks for your help. Please take all the time you need

1. Let's first look into the relation of lipid biosynthesis and peroxisomes -
According to this article, the main functions of peroxisomes are-

As you can see most of the pathways that occur are oxidative in nature. That is,     the main function is breaking down lipids and not their synthesis. The reason why peroxisomes are also known as Oxidative organelle. Even though peroxisome is involved in the synthesis of plasmalogens, and it has no requirement of hydrogen peroxide for the same.
Endoplasmic Reticulum is the organelle that synthesizes majorly lipids. So, the deficiency of hydrogen peroxide won't affect lipid synthesis.
2. Next is the role in the pentose phosphate pathway-
The major pathway for glucose catabolism is glycolysis. The location of the glycolytic pathway is the cytoplasm of the cell. Parallelly to glycolysis, PPP also runs in the cytoplasm. However, the major role of PPP is anabolic and not catabolic. The PPP is generally studied in 2 phases -

The oxidative Phase (Generation of NADPH when Glucose is converted to 6-phosphogluconate)
The non-oxidative phase (Synthesis of 5-carbon sugars)

As this article states

The glycolysis and pentose phosphate pathways (PPP) are tightly connected. The glucose entering the in cell membrane is rapidly phosphorylated by HK and converted to G-6-P. The G-6-P is metabolized either by the glycolytic pathway, generating pyruvate and lactate, or by PPP to produce NADPH. The F-6-P and G-3-P generated from the non-oxidative branch of PPP can enter glycolysis

Also,

The R-5-P, a product of oxidative PPP, is converted into G-3-P and F-6-P by transketolase (TKT) and transaldolase (TALDO1), creating a reversible metabolic link between PPP and glycolysis

Since, both of these metabolic pathways are highly connected to each other. The major location for PPP is the cytoplasm. However, PPP also do occurs in plastids and peroxisomes.
Again, if there is a deficiency of hydrogen peroxide in peroxisome it won't affect the PPP.

Role in the breakdown of fatty acids

As this article states -

Oxidation of fatty acids occurs in multiple regions of the cell within the human body; the mitochondria, in which only Beta-oxidation occurs; the peroxisome, where alpha- and beta-oxidation occur; and omega-oxidation, which occurs in the endoplasmic reticulum.

Also, as mentioned above peroxisomes are the main location for fatty acid oxidation.
Let's take a look at how hydrogen peroxide has a role in this catabolism.
From Lehninger's Principles of Biochemistry(7th edition) -

In the very first oxidative step (for mitochondria), the H-electron is transferred to oxygen, and water is produced.
In the case of the first oxidative step (for peroxisome), the H-electrons are first transferred to FAD, making it  FADH2 then to oxygen, generating a hydrogen peroxide molecule. This biochemical reaction is catalyzed by H2O2 producing enzymes. This H2O2 is further broken into water and 1/2Oxygen by catalase, thus canceling out the reactivity chances of H2O2 with any other molecules.
If there is a deficiency of H2O2 in peroxisomes, that means any of the enzymes catalyzing the formation of H2O2 is deficient. In such a scenario, the first oxidative step of fatty acids breakdown won't take place in peroxisomes. This will eventually lead to the accumulation of long fatty acids chains in peroxisomes and further apoptosis.
Mitochondria's main role is in energy production and not fatty acid oxidation, though it will help in fatty acid oxidation but the number of fatty acids oxidized only by mitochondria will be very very less and the net result will be an accumulation of fatty acids.

Wow this is a lot of information but it explains everything very well. Thank you so much

source: Stack Exchange

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What were the three dinosaur evolutions and do they imply that bipedalism could have evolved multiple times in hominins?
At this pop-sci article transcribing an interview with Jeremy DeSilva, they state:

"If we’ve learned anything about evolutionary trends, it’s that good
ideas evolve over and over again. For instance, the evolution of
feathers and dinosaurs independently evolved three times. You could
get the independent evolution of bipedalism multiple times."

I have two questions:

What are those three events of the independent evolution of dinosaurs? Also, are there other such events that are suspected but are not as well understood?

Is he correct in using these independent dinosaur evolution events as reason to imply that bipedalism in hominins could have evolved multiple times? That is, are there nuances/details regarding the dinosaur evolution events that constitute important differences compared to the case of bipedalism in hominins?

Note: I used the word hominin here because that is what Jeremy DeSilva used in the cited interview, but I understand that may affect the answer to my question as chimps are also bipedal, but feel free to inform me!

"Dinosaur", when used properly, refers to a clade. There's no way for a clade to evolve multiple times, or even to really evolve at all as something that happens; it's just a name for a group of descendants sharing a common ancestor.
I'm guessing instead that it's an incorrect transcription of "feathers in dinosaurs", since in and and sound quite similar out of context; that is, that something structured like a feather evolved three times in the dinosaur lineage.
I know little to nothing about this area, but Wikipedia's article on feathered dinosaurs suggests that this is a bit unresolved:

It is not known with certainty at what point in archosaur phylogeny the earliest simple "protofeathers" arose, or whether they arose once or independently multiple times.

There are feathers observed in multiple lineages of dinosaurs, but it seems most plausible that they all came from the same origin rather than independently. For the intervening species it may be that either they lost the feathered phenotype or that there is simply not fossil evidence of feathers for those species.
As for bipedalism, well, we don't really need any feathers to reason that a trait could evolve more than once. Flight itself is a simple example: there are flying insects, flying birds, and flying mammals (bats), all who evolved flight from previously flightless ancestors.
The most direct example, though, is bipedalism itself: there are many bipedal dinosaurs, including modern birds. Human bipedalism evolved separately from non-bipedal mammals. Arguing whether it's happened multiple times among the apes is another story, that has little to do with any examples from other clades or other traits except analogy. Certainly, other apes locomote on two legs at times, but none of them walk quite the way humans do. If you want to argue that feather evolution involved an earlier "protofeather" that then separately evolved into a full-fledged (hehe) version multiple times, then maybe that would relate to a "proto-bipedalism" (as observed in apes) that could result in multiple "truly bipedal" lineages, but one would need further evidence to support that.

I'd add that there's a good chance that bipedalism in dinosauria as a whole, while it might have evolved separately, there were vast expanses of time (conservative short 166 million years) between the beginning and end of dinosaurs... something Apes haven't had (yet - 25 million years)

And don't forget flying pterosaurs :-)

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Which hornet-like insect is this?
This insect flew through my open 10th floor window, around midnight.
Its flying pretty fast for insects, and bumping into the ceiling a lot.

Location: southern Germany.
For me it looks almost like a hornet, except for the eyes, which in my opinion are way to big for hornets.
The wire mesh in the background has a 12mm spacing.
Any guesses?

Not a hornet at all, nor any Hymenoptera but rather a Diptera. As you suggest, the eyes as well as the wing structure give it away.
It looks like a horse fly, possibly Tabanus sudeticus or Tabanus bovinus based on the large size and coloration in the abdomen.


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Why does open olive oil keep so long?
This is a question about the biology of microorganisms, not about food safety.
While most of our foods spoil quite quickly (it is recommended to throw food away after 2h in the danger zone), for some oils this is not the case: for example, opened olive oil may be kept for 18 or more months at room temperature.
This seems to indicate that while there are plenty of microorganisms around, pathogenic or otherwise, which readily feast on carbohydrates or proteins, there do not seem to be that many (or at least not in practically relevant amounts) that can metabolize our food oils, while our stomachs have no problem with that.
Why is this? Is it hard for microorganisms to break down the fatty acids (if so, for what reason), or do these oils usually have secondary constituents which are poisonous to microorganisms, but not to us?
Note that some bacteria can use fatty acids as energy source; that makes it even more interesting why it doesn't occur in our kitchens...

Oil Rancidification is a good read: https://en.wikipedia.org/wiki/Rancidification

There are plenty of foods that conserve long time after being open - sugar, flour, cereals, water, etc. This is to say that one needs to narrow the class of foods in question - which may already contain the answer.

That was a very interesting read, thanks @Science123, though it looks at it more from the point of view of the oils themselves (ie., also processes like autoxidation which do not involve microorganisms). Like the link I have in the question it also mentions E.Coli, and that there are natural anti-oxidants like Vitamin E... now the question remains - are these oils so chok full of anti-oxidants/microorganism killers that those have no chance; or are there little no no microorganisms that can survive on oils in the first place (and if so - why)...

True, @RogerVadim, but I fear if I open up the question for all kinds of stuff ("why do some kinds of foods not spoil") it may be a little too generic...

Bacteria and other Microorganisms are mostly water, and to replicate they will need more water. The water they need is not present in olive oil. Salts and other required elements are also not present in olive oil, at least not in sufficient quantities to  support proliferation of microorganisms.
Our stomachs indeed have no problem metabolizing oil, but if you had nothing else to eat or drink, you would die in short order.

Oh man, in hindsight the water aspect really seems quite trivial, and incidentally also answers why stuff doesn't grow on very dry stuff in general (pure sugar etc.). Thanks for opening my eyes!


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At what point in evolution is a new species identified?
As we know, a change in allelic frequency leads to evolution, and as these changes accumulate a new species is created.
My question has two parts -

A classical definition of species which is now not accepted everywhere:
Two different species are the populations that has lost the ability to interbreed among themselves to produce viable offspring.  I have read some of the answers on stack exchange addressing the genetic reasons for hybrid sterility. They frame faulty pairing in meiosis as the main reason, but if the genes are on the same loci in two different closely related species how does a change in allelic frequency lead to faulty meiotic pairing in the germ cells of the hybrid?

In the divergence of two populations sharing a common ancestor, allelic  frequencies are changing, but at what point are the populations called two different species?

Does this answer your question? How is genetic speciation defined? To quote one of those answers: "It turned out that the main differences between the two genomes were clustered around regions where chromosomes were rearranged. Although indicative of the cause of speciation, it can nonetheless also be the result of it. We can never be sure." Chromosome rearrangements are of course one of the most obvious mechanisms for bad meiotic pairing and non-disjunction.

what do you mean by chromosome rearrangement can you define and elaborate the process by which it happens?

ok this answers the 2 nd part of my question that when can we say two population are no longer the same species (:In other words, when two suspected sub-species are not able to produce viable offspring, they can be considered to be two species." but i was looking into the biochemical or genetic reason and their relation with changes in allelic frequency, though its a good answer.

Chromosome rearrangement: when structure of chromosomes changes. This is a very large and complex field of inquiry, and there are many mechanisms by which it happens. That is a large question in itself, I recommend doing background research and possibly asking a separate question if the term is unfamiliar. 2. Biochemical/genetic reason for speciation: I think that the take-home message is the one in the linked answer, which is that there is no single mechanism by which species are defined. I would consult the linked answer for more information about how species are defined.

Directly to your interest in allele frequencies: I don't think that changes in allele frequencies are going to tell you much about speciation. I think that they are an inexact and rather generic description of an extremely complex and context-specific process.

Please take the [tour] and then consult the [help] starting with [ask] questions effectively on this site. From this you will see that we expect questions to be focused (including one question per post), well-researched (in particular, you need to look for overlapping questions on this site), and clear. — In one sentence  you wrote "if the genes are on the same loci", which doesn't seem to mean anything, and "how does a change in allelic frequency lead to faulty meiotic pairing", which assumes something that isn't true. I strongly encourage you to do some background reading/research. ...

... I have found Khan Academy to be very helpful for learning the basics of a subject. You can then move on to Understanding Evolution from the University of California, Berkeley. After that there are many free textbooks available at the NCBI Bookshelf and many other online resources.


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Besides fats, proteins, and carbs, what compounds can the body use for energy?
What kinds of chemical species that do not belong to the category of fats, carbohydrates or proteins can the body metabolise?
Clarifications: By metabolise, I mean extract energy from (e.g. as ATP). The chemicals would be ingested as “food” regardless of whether they occur in natural dietary nutrients.
I already know of one, ethanol.
At a wild guess, I suspect the body can extract energy from acetate and citrate too.

@classy_BLINK I'd be very impressed if you could find me somebody who could ingest enough of those to obtain food energy from them without instantly ODing.

I suspect this question needs a little more detail to be answerable. Are you specifically after things that a reasonable user might think of as 'normal food'? We metabolise pyruvate to release energy, and you can buy it as a supplement. If pyruvate is in, then we can start with a list of most of the intermediate metabolites in the Krebs cycle.

Also: human bodies only?

@bshane Yes human bodies, and no it doesn't necessarily have to be 'normal food'. Sounds like the intermediates of the krebs cycle would count. I'm interested in anything a human can extract a non-negligible amount of food energy from without dying in the process. By 'non negligible' I mean at the very least something that would stave off death for a starving person in the short term.

I see two ways to approach this. First, molecules used as part of respiration to store energy as mentioned by bshane. Alternatively, it may be worth considering environmental context (e.g. what other energy sources would humans naturally intake; think chemosynthesis in the deep ocean). Sure, supplementing a human body with pyruvate and/or friends may fit the bill, but (as hinted by classy_BLINK, it would seem likely that having that as a sole (or majority) form of energy intake would probably cause significant dysregulation of metabolism.

The phrase “food energy” means nothing to a biochemist. “Energy” would suffice or ATP if you wish to specify the common chemical intermediate. It appears from the comments(Krebs Cycle intermediates) that you mean food to indicate the form in which the “chemical species are supplied. In which case I suggest “ingested” as a better way of putting it. I will try to edit it, but as there is a bounty on it I may not be able.

@David I stipulated 'food energy' because the energy listed on Nutritional Information boxes is usually derived from calorimetry -i.e. burning the food in the lab and measuring the heat coming off. I wanted to head off any 'look at the back of the packet' comments.

There are two significant energy sources for humans besides fats, carbohydrates, and protein listed in this USDA report that I found:

Organic acids: these are compounds like citric acid and malic acid that make up a small but significant portion of the energy content of many fruits and some vegetables. The energy content is in the range of 2-4 Calories per gram, so slightly less than from protein or carbohydrates.
Alcohol provides about 7 Calories per gram.


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Is 'constitutive effect' the proper term for explaining a biological effect that occurs due to the constitutive knockout of a gene in a mouse?
I am working on an experiment involving the analysis of expression of a protein X in wild-type (+/+) and knockout mice (-/-). In the knockout mice, the gene of interest has been constitutively knocked out. For both genotypes, I am analysing postnatal day 2 (P2) and postnatal day 10 (P10) mice.
If in the knockout P2 and P10 mice, the levels of protein X are significantly increased compared to the wild-type P2 and P10 mice respectively, one could say that this effect could possibly be due to the gene of interest being knocked out. However, I was wondering, is 'constitutive effect' the proper terminology to explain a biological effect that occurs due to a gene being constitutively knocked out?
Any insights are appreciated.

"...one could say that this effect could possibly be due to the gene of interest being knocked out." Assuming the wildtype and knockout mice share a common genetic background and appropriate controls are performed, you should be able to say this with more confidence than "possibly."

Not necessarily... knockouts are a rather crude and problematic tool for studying regulatory systems. Have you read "Can a biologist fix a radio?"

I have generally seen the term "constitutive" used to refer to a "always on" expression of a gene with no anticipated regulatory interaction. Thus the term "constitutive knockout" seems a little bit oxymoronic to me, and I would tend to prefer a different term, like simply "knockout" or, if you really need to differentiate from conditional knockout, "unconditional knockout."
Likewise, if you wrote "constitutive effect", I would tend to interpret that as an effect of a gene being on, not a gene being knocked out. And even then I would find the terminology unsatisfying, as again it's mixing ideas of regulation (effect) and non-regulation (constitutive).
I would suggest you keep the terminology more direct and simply refer to the knockout itself, e.g., "knockout effect", or "effect seen in knockout mice".


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Why/How can Hydrophobic things pass the lipid bilayer?
I’m just looking for a simple answer for this question. I’m in Bio 10, and don’t know the in depth stuff. So the lipid bilayer is hydrophilic and the ends, but hydrophobic in the middle; so how can the hydrophobic substance pass through the phosphate head in the first place? If hydrophobic substances can pass through, shouldn’t hydrophilic substances be able to pass through as well? TIA


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Do mutations that cause the loss of a complex trait occur more often than mutations causing gain of a complex traits?
The Wiki entry on the evolution of biological complexity states that "[m]utations causing loss of a complex trait occur more often than mutations causing gain of a complex trait". There is no inline  citation supporting this claim, nor could I find anything of the sort in the bibliography. So I was wondering whether this is thought to be the case and what key work has been done concerning this claim i.e. major papers either for or against the thesis.

Many mutations are needed for complex gain of function. Only a tiny mutation is needed for loss. Only one change is needed to break a long chain of synthesis. For example, the chain needed for melanin sythesis - see albinism http://www.albinism.org/information-bulletin-what-is-albinism/

@PolypipeWrangler While the principle you mention is a good general guide, there are exceptions. For example, a single mutation in a regulatory region can change the location and/or timing of expression of a protein and produce complex changes. See the often dramatic results of mutations in insect Hox genes.

While I don't have a citation at hand, I don't think that one is needed. The principle follows directly from the notion of mutation in a complex system.  Put simply, once you've got a functional complex trait in play, there are many ways to break it and much fewer that can further improve it.
This fact is often mis-interpreted by creationists to claim the evolution of complex traits is impossible. With a population under selective pressure, it doesn't matter if more mutations are negative than positive, because the positive traits produce many more descendants.
To take a current example, the SARS-CoV-2 virus has an important complex trait in the form of the spike protein that enables it to invade human cells. An infected person produces a vast number of copies of the virus, many of which have mutations that destroy the functionality of the spike protein. So those mutations disappear immediately, while the non-mutated or neutrally-mutated copies infect as usual and the rare improvement in efficacy brings us developments like the Delta strain.

+1 I think it is worth qualifying what is meant by more often. In a particular individual the loss of trait is certainly more likely than the gain. On the other hand, the direction of evolution as a whole demonstrates acquisition rather than the loss of traits: complex organisms evolved from simple ones, contrary to the creationist argument.

@RogerVadim "Direction of evolution" and "creationist argument" should have some scientific definitions attached if they're to be posted here, I think. This question seem to be simply about the mutation event (based on the context of the referenced wiki quote).

@Armand I am saying that "more often" is both correct and wrong, depending on what one is talking about.


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Is the central sulcus the boundary between basal and alar derivatives?
The dorsal part of the nervous system typically gives rise to sensory structures, and the ventral part gives rise to motor structures.  Because the central sulcus marks such a functional boundary, I had assumed it was an example of this zonation ... however, recently I didn't find any source to defend this position.  (I would have been sure that hunting for "fate map" and "central sulcus" would pull up something informative...)  Some of the embryology, in which I think a trace of a central sulcus might be apparent quite early, can be seen at UNSW, but none of the embryology images I considered really seem usable to answer the question.
*Note: "Central sulcus" is referenced as a visible marker for the boundary between motor and sensory functions.  Answers that trace the origin of this boundary in species where it is not marked by a sulcus are also welcome.

The basal and alar plates have an important sensorimotor separation of duties in the spinal cord. I don't see any reason to apply this to the cerebral cortex that develops from the forebrain - you're probably not finding anything about this because people don't concern themselves with alar/basal plates in the front of the brain.
Importantly, the neocortex is pretty evolutionarily new. You're placing strong developmental purpose on a sulcus that doesn't even exist in the evolutionary ancestors of humans. There is no such separation between sensory and motor cortex in a mouse, for example.
See this sagittal view of a forebrain:

(image from Medina L. (2009) Evolution and Embryological Development of Forebrain. In: Binder M.D., Hirokawa N., Windhorst U. (eds) Encyclopedia of Neuroscience. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-29678-2_3112)
The neocortex is just a small slice situated at the dorsal surface of the forebrain (yes, it does wrap around the entire dorsal surface and extends along the lateral sides, but that doesn't make it anything but dorsal). There is no trace of any dorsal or ventral embryonic origin within the neocortex. The dashed line that roughly separates the dorsal and ventral parts of the CNS ends in the diencephalon; in this view, all of the neocortex, including motor cortex, is part of the dorsal "sensory" part of the brain.

From the papers and images I'm seeing online, such as this one, I have the impression that the mouse forebrain has a relatively similar overall organization with motor areas in a frontal lobe.  (The motor barrel is specific to whiskers, and RFA's exact nature seems to be subject to interpretation, but the overall emphasis seems the same)  Also, I don't see how you can say the region is entirely dorsal but also that there is no trace of dorsal embryonic origin.

@MikeSerfas Yes they have a motor cortex. They do not have a central sulcus, or really any sulci or gyri besides one, the rhinal fissure. The general positions are like humans but there are no "lobes", we only call them that to reference primate brains. I'm saying there's no dorsal/ventral origin separation for cortex. It's not relevant. If you find somewhere that says it's relevant, great, but you shouldn't just look at pictures and guess.

Well, that's why I asked here. :)


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What controls the growth of a body?
Everything in our bodies is made of cells - bones, muscles, brain, blood. How do cells know how to build a body? Granted, each cell has a blueprint of the whole body in its nuleus, the genome. Does that help the cell know where it is in the grand scheme of things and how it should behave (divide?) for the end result to look like a human body?
If someone told ten million people to form the word "Help!" that's 100 miles wide and each person got the exact blueprint of what the end result should look like, I don't think the aliens would see a convincing message in a few months or maybe even years.
If those people are to finish their task in any forseeable future, they need some kind of a feedback loop. For instance, they could build an app that showed everyone's position on the map, so they could say "Hey, that blob looks like they're trying to be the dot in the exclamation mark. I need to move 400 meters to the south-west if I want to join them."
Do cells have similar feedback loops? Or am I too naive to think that individual cells have any say in how our bodies are built? If it's not the cells, then what is it that controls the growth of our bodies making sure we don't grow a second head and everything works in perfect harmony? Obviously, this doesn't work 100% of the time - that's when we get cancer or Siamese twins. But it works most of the time.
How does the body do it? What and where is the conductor of this billion-cell orchestra?
I am not a biologist, so please be condescending. After all, the question What controls the size of breasts? got a decent answer. I don't see why mine shouldn't.

Welcome to Biology.SE. Unfortunately this is not a good question for this site because it is too big. From the [help/dont-ask]: Your questions should be reasonably scoped. If you can imagine an entire book (or this case an entire library) that answers your question, you’re asking too much. To get some idea of the size this field of research you can search on this site for the tag 'development', which is relevant to your question (currently >200 questions). IMO, if you have a strong interest in this subject you should start with the basics and work up to this very big question. ...

... I have found Khan Academy to be a good way of getting a quick introduction to an unfamiliar (or mostly forgotten) subject area (I used them to relearn the basics of calculus). There are also many free textbooks available at the NCBI Bookshelf. Other reading you might find interesting includes this — try searching for "developmental-biology for computer-scientists" to find similar material. Hope that helps.

so basically you want us to sum up all of embryology for you? note the question about breasts is about a specific tissue. your question is far too general there is no conductor other than your DNA each tissue is controlled in a different way by different gradients and feedback loops. try starting here https://en.wikipedia.org/wiki/Embryology

The answer to your question is huge and still evolving, involving whole fields of scientific research.
The general process of how cells develop macro-structure forms is known as morphogenesis. Within that realm of study, the science of "evo-devo" (evolutionary and developmental biology) is closely tied to the question that you've asked, as it turns out that the molecular basis of body-plans and how evolution works are closely tied together.
I would recommend that a good place to start is the popular-science book "Endless Forms Most Beautiful", by Sean Carroll, which provides a nice introduction, overview, and good intuitions for the non-biologist to start to understand what is known about this topic.

acapellascience's youtube channel has a song called evo-devo that nicely summarizes Carroll's book.


text:
Do all tumour variants affect the disease pathway
I have analysed some lung tumour samples for somatic variants which generated a list of genes affected by those variants. I tried to analyse KEGG pathways to see what could they disrupt. However, many of the affected genes cause neurological diseases and some cause congenital structural defects. I believe these genes would not be expressed given the location of the tumour. I suppose they will be inaccessible so they would not affect the individual. Is it true or there's something else going on?

Biology is complicated. It's hard to say without looking at the list of genes. Or indeed, even with the list of genes.
What you are calling a "disease pathway" might instead just be a list of parts that cause cancer when they are broken. There is no guarantee that that list of parts is complete. But as you seem to guess it is hard to conclusively demonstrate causality without either experiments or corroborating information (such as finding genes previously known to cause cancer). For example, this page writes:

A recent study published in Nature Genetics, for example, found 10 new variants associated with lung cancer, and studies published in Nature and Nature Genetics found 72 new variants associated with breast cancer.

In the case of breast cancer, 10 of the risk variants are associated specifically with the risk of developing estrogen receptor-negative disease, which tends to have a poor prognosis and for which few genetic influences were previously known.

So only 10/72 of their variants fit into a clear mechanism! This is pretty standard in the field, is my understanding.
Some people have tried to increase their power in GWAS to detect functional associations by leveraging biological associations between genes, for example protein-protein interactions.
While this type of analysis is convenient for variant interpretation, its actual truth is difficult to interpret (for me at least). But it might provide some path forward.
Update
As an aside: you should be able to directly check the expression of genes. You don't have to guess/doubt that the genes are expressed. There are anatomical atlases of gene expression, though in cancerous dysregulation some additional genes may also be expressed. Alternately, you could just directly measure expression, assuming that you still have samples.

Is this what you're thinking of?  They write they have a package including networks for small cell lung cancer available for download, though I was getting a "page can't be found" just now.

@MikeSerfas I wasn't thinking of that specifically, more reflecting that this is a generic method that people use for association results when there isn't a clear pathway. However, that ref does seem pretty relevant to the asker. I do see that they include a ZIP archive of matlab code, which I was able to download (proprietary, so possibly not too useful): https://www.nature.com/articles/nmeth.2651#Sec24


text:
Are there some natural instances of thermosensitizer?
Let's define thermosensitizer as any chemical or biological agent that can sensitize the cells to heat. In lab setting, thermosensitization seems to be achievable, such as by inhibiting chaperone activity.
I wonder if in nature there are some instances of thermosensitizer? Specifically, the question is not concerning the various regulatory mechanisms of the cells to survive heat. It's more about if some organism can exert/secrete chemicals on another organism to make the latter more sensitive to heat, for example in self-defense or for killing.

Geldanamycin/radicicol would be examples. They are both Hsp90 (protein chaperone) inhibitors. There is a lot of literature on their biological effects (see references therein), specifically their role modulating genetic interactions and also as chemotherapeutic agents for killing cancer cells.
Both of these natural compounds are created by microbes as antibiotic chemicals for interaction with other organisms.


text:
Does it make sense to say that microtubules are arranged in a ring around the cell periphery?
I am reading a journal paper and it is about how the organisation of microtubules are altered in CHO cells that overexpress microtubule-associated protein Tau.
In the paper, the authors found that overexpressing Tau in CHO cells resulted in changes in the organisation of microtubules. In the paper they state:

Non-transfected, interphase cells contained typical radiating arrays
of microtubules that often could be seen to emanate from a microtubule
organising centre when labelled with the tubulin antibody. However,
transfection of tau into these cells dramatically altered this pattern
of labelling. In cells expressing high levels of tau (as judged by
intensity of fluorescence staining), bundles of microtubules could be
discerned which often formed a ring, or spiral around the
circumference of the cell (Fig. 1A,B).

I have described what the authors have discovered in the tau-transfected cells in my own words: "In cells overexpressing Tau, microtubules were bundled and arranged in a ring structure around the cell periphery".
I have read online that the cell periphery is the part of the cell encompassing the cell cortex, the plasma membrane and any external encapsulating structures.
By saying that the microtubules were arranged in a ring around the cell periphery, I want to convey that the they are arranged in a ring around the perimeter of the cell. However, I was wondering if using the phrasing "around the cell periphery" makes sense, because I do not want people to misunderstand my sentence and think that I am saying that the microtubules are arranged in a ring outside the plasma membrane by using the word around.
Any insights are appreciated.

I read periphery as meaning outside and proximal.  So I would interpret around the cell periphery as referring to something that is closely associated with but external to a cell.

Are you asking because you are trying to avoid plagiarism? Otherwise why not use the original phrasing?


text:
In fluorescence microscopy images what is meant by the term "puncta"?
I am reading papers where confocal fluorescence microscopy images were analysed. In many of the papers I see the term "puncta" being used when researchers analyse the colocalisation between 2 proteins. For example, in the linked paper:

In addition, many C1q-positive puncta in the IPL were associated with
synaptic puncta identified by double immunostaining with synaptic
markers such as PSD-95

I am not sure what is meant by the term "puncta" in the context of immunocytochemistry. I have read that the general definition for puncta is a small, distinct point. However, I was wondering whether puncta is a synonym for clusters of a protein (e.g. in the example above, does synaptic puncta refer to clusters of the PSD-95 protein?)
Any insights are appreciated.

I have read that the general definition for puncta is a small, distinct point.

That's correct. From my understanding, puncta are dots.

However, I was wondering whether puncta is a synonym for clusters of a protein

In the context of fluorescence microscopy, a punctum (plural puncta) does not specifically refer to the aggregation of proteins. Any small, distinct points in the field of view may be called puncta. I like to think of puncta in contrast with foci, which I generally understand to be regions of interest, though, in practice, the two terms are often used interchangeably. Here are some examples from the literature:

The phosphorylation of H2AX at Ser139, resulting in the formation of γH2AX puncta in the nuclei, is an early event in the cellular response to DNA damage.

Chiu YH, Hsu SH, Hsu HW, Huang KC, Liu W, Wu CY, Huang WP, Chen JY, Chen BH, Chiu CC. Human non‑small cell lung cancer cells can be sensitized to camptothecin by modulating autophagy. Int J Oncol. 2018 Nov;53(5):1967-1979.

It is well known that histone H2AX becomes phosphorylated at Serine139 to γH2AX immediately after irradiation, and involves a large chromatin region of up to ~ 2 Mbp, thus forming distinct μm-sized foci at the sites of DSBs.

Memmel S, Sisario D, Zimmermann H, Sauer M, Sukhorukov VL, Djuzenova CS, Flentje M. FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy. BMC Bioinformatics. 2020 Jan 28;21(1):27.

My impression is that "puncta" is used in fluorescence microscopy (and autoradiography perhaps) when points are are indistinguishable from a single point source, but because it's plural they're talking about a bunch of dots from the perspective of the dots. When they write "foci" they're talking about a region that light emits from, without specifying whether they have observed individual puncta or not. You might get different descriptions of the same organization just because people think differently, or because of different imaging techniques. Or I might just be reading too much into it.

I agree with that. Puncta are dots. Foci may contain puncta, or foci may just be a diffuse but noticeable region of fluorescence.


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When Bacillus subtilis form spores vs die?
In my understanding:
sporulation in Bacillus subtilis involves the differentiation into two cell types, the endospore, and the mother cell. The endospore coat is a multilayered shell that protects the bacterial genome during stress conditions and is composed of dozens of proteins. However, I also read about how Bacillus subtilis could die.
Q: When do Bacillus subtilis cells die vs form endospores? Also, could there be dead endospores?

Minor correction first: Bacterial endospores don't result from one cell differentiating into a different cell type. An endospore is not a cell type, but rather a protein structure that first forms inside of a mother cell, carrying all of the necessary machinery and genetic material to remain viable outside of the mother cell and eventually form a new cell when it encounters the right environmental conditions. In a sense, it's more like a mother cell becomes an endospore through the process of sporulation, which (with any luck) eventually becomes a new vegetative cell through the process of germination.
Bacterial endospores tend to form when cells encounter environmental stresses (like lack of nutrients, changes in pH or temperature, etc). Generally speaking only a portion of bacterial population will sporulate under a given set of conditions. However the remaining cells don't necessarily die right away. They may remain viable for quite some time, depending on how much and what type of stress they are experiencing.
Sporulation efficiency (the percentage of cells in a population that sporulate) is governed by a number of different environmental and genetic factors. Some organisms require specific nutrients or vitamin cofactors to sporulate efficiently. Others may require a specific pH range temperature. And different strains of a given organism can have wildly different sporulation efficiencies, making it hard to provide a very specific answer to your first question.

Q: When do Bacillus subtilis cells die vs form endospores?

The broad answer is that cells sporulate when they encounter the proper environmental cues in a medium containing all of the required nutrients in the correct amounts. And the ones that don't form spores don't necessarily die (it's not often an either/or scenario). You can look at a sporulation protocol for B. subtilis to get an idea of what makes them sporulate (see page 9 of this document).
Because sporulation requires time, vegetative cells will simply die if you assault them with something that kills them fast enough, or otherwise prevents sporulation from happening. But in most environments (outside of a lab), bacterial populations are heterogeneous and will likely already consist of a mixture of spores and vegetative cells. So when you try to kill them with something like that only kills vegetative cells, like a solution of ethanol, you are simply killing off the vegetative cells, leaving behind a preexisting population of spores to germinate and grow when conditions change again.

Also, could there be dead endospores?

Yes (assuming you consider endospores to be living). In practice, and population of dormant organisms will have some members that are no longer viable. Spore stocks in long term storage will slowly lose viability over time. There's also a lot of basic and translational research on how to most efficiently and effectively kill bacterial spores, especially those of sporulating pathogens in sensitive environments like hospitals or assisted living facilities (the answer is bleach. It's always bleach).


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Tiny Green beetle
I have some tiny, bright-green beetles on Granny Bonnet seed heads in Cornwall, UK. The insects have black heads and 3 black/yellow stripes across the back. They are ladybird shaped but much smaller. Any ideas what these might be?

I can’t help you personally, but I recommend trying the app Seek on the App Store. I find it to be very helpful and it probably could identify them. I recommend taking a picture and then going to images in the identification camera, it is much faster.

You could use an app and self-answer your question if you get a result, but I do think having a good quality picture will greatrly improve your chances of getting an answer here! See also https://biology.stackexchange.com/tags/species-identification/info

My guess is the nymph of some species of shield bug, such as the Common Green Shieldbug (Palomena prasina)

 Source: Wildlifeinsight.com
According to Wikipedia:

Green shield bugs are a very common shield bug throughout Europe, including Great Britain & Ireland, and are found in a large variety of habitats, including gardens.


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If crossing over can cause formation of new allele, can it affect Hardy-Weinberg equilibrium?
I was reading about Hardy-Wienberg equilibrium on Wikipedia  and there are seven assumptions underlying HW

It is mentioned that sexual reproduction one of the assumption and is a must for HW, but according to some answers given here on Biology STack exchange crossing over in sexual reproduction can result in exon shuffling
here is the answer I am referring to
so my question is-
1.can  exon shuffling  cause a new allele to appear in the population?
2. If a new allele can appear in the population during the cross over or due to crossing over as it is a random process that will surely change the allelic frequency so how can be sexual reproduction can be a underlying assumption for HW? it should be in the list of things that can affect Hardy-Wienberg like mutation and sexual selection
3. Does in majority of cases crossing over only causes reshuffling of allele but not the formation of a new allele? is mutation by crossing over is rare?
4. Can Independent assortment and Linkage have any effect on Hardy Weinberg law?

I'd consider creation of a new allele by intragenic crossing over a mutation.  HW was developed over 100 years ago, before the molecular nature of the gene was known, so it was based on Mendelian genetics. Normally, recombination rates within a gene will not be significant.

Reading a bit futher in the Wiki entry, "Mutation will have a very subtle effect on allele frequencies. Mutation rates are of the order 10−4 to 10−8, and the change in allele frequency will be, at most, the same order. Recurrent mutation will maintain alleles in the population, even if there is strong selection against them."


text:
Can you calculate the coefficient of inbreeding (F) without a family history?
Apologies in advance, this question may be completely obvious.
Say, I didn't have a family tree for two individuals. Could I calculate their coefficient of inbreeding? If not, is there a good proxy for it or an alternative way to calculate it?

Yes.
These days inbreeding coefficients are generally computed from observed gene frequencies, not from pedigrees.
From this review:

Inbreeding coefficients are defined in terms of the
probability of identity in state of different pairs of genes.
Here the probability of identity in state is simply the
probability that two genes are of identical allelic type.

Thank you very much. One further question. How expensive would it be to calculate the coefficient of inbreeding for a random couple? I'm an Economist and this isn't my domain of expertise.

@anonymousquestionbio1994 It really depends on the degree of precision that you want, density of information, extensibility, etc. I suggest doing some background reading on the topic of experimental design in the field: https://www.frontiersin.org/articles/10.3389/fgene.2020.00870/full, https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-12-16-0425-RVW

Thank you again! Will certainly be reading this!


text:
In the Kok cycle occurring in Photosystem II's Oxygen-evolving Complex, what exactly does P680 do?
I've been reading up on the oxygen-evolving complex using a few sources, but am a non-biology major so my understanding might be somewhat/very flawed. I've been using this source mainly:
https://faculty.missouri.edu/~glaserr/3700s13/PS-Review2.pdf
and have so far gathered that, along phases S0 to S4, the Mn complex holds onto the 2 water molecules while it is "oxidized" by P680 with the help of tyrosine Yz; instead of oxidizing water directly, P680 oxidizes a total of 4 Oxidizing Equivalents, which act as "stand-ins" for the redox reaction involving water. At the final stage, the Mn complex has a total charge of 4+, which then causes the 2 oxygen atoms (from 2 H20) to give up their  electrons and turn into molecular oxygen, something this source also says:
https://www.life.illinois.edu/crofts/bioph354/lect25.html
My preliminary question is, is my understanding correct at a basic level? And if it is, then what is P680 doing?
We've been told that it's one of the strongest organic oxidizing agents, which made me think that it stripped the hydrogen from H20 immediately, but instead it seems like the "splitting" of water occurs in the Mn complex thanks to the 4 oxidizing equivalents.
Is P680's role still essential in this process? As in, is P680's strength the only natural thing that can oxidize the Mn complex at each step so that it eventually splits the water? Or am I misunderstanding the "water-splitting" step entirely?


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Why do colors clash in your brain?
Wen pairing two or more colors together, some "clash" or cause a effect visually where the two colors meet. To me it appears to be a black line between the colors or shading when in fact there is not. I grey scaled the picture to confirm. In dogs, they would just see different shades of grey and this effect would not affect them. So, what is this that which make this effect in the brain?

Could you explain what you mean by "clash"?  I don't see any real difference between the colored image and the grayscale one.  Maybe it's something specific to YOUR brain - or maybe I'm the odd one :-)

@jamesqf there is an optical illusion of a very thin black line between the red and the blue sections in the top image. There is less contrast between the two gray tones in the bottom image, so this illusion doesn't appear as evident (at least to me). Do you know if you have some version of color blindness?

@MattDMo: No, I don't have color blindness, and I see that "illusion" on the gray scale image as well, though not as strongly.  If it is an illusion, and not an artifact of whatever created the image,  But I haven't tried blowing up either image myself.  I would suspect, from having done some work with computer feature recognition, that it's an artifact of higher processing levels segmenting the image into recognicable features, but I don't actually know.

@jamesqf it is indeed an artifact https://i.stack.imgur.com/3E7PO.png

Magnify your image.
I just put it in GIMP and it is clear that there are several pixels in the red and the blue near the border which are a darker color than those adjacent - the drawing program must be responsible.
Lateral geniculate nucleus
That said, differences of red and green hue are handled more in the parvocellular layers of the LGN, while grayscale differences are handled more in the magnocellular layers, with blue cones contributing to the koniocellular layers the most.  In your images, all three are involved.  There are some individual differences reported between these regions and their timing of activation in regard to dyslexia - it's a hot topic, and these variations seem to be the explanation for that perplexing condition.  I'm not going to point to any specific paper because I'm not sure how to interpret the "clashing", but there's some interesting reading there!

Your first paragraph about magnification is not, I think, relevant. What you are observing is something called “anti-aliasing, which is a way in which a smooth, rather than a jagged, border is produced (in the brain). The visual effects need not be generated by computer — they were and are a staple of certain printed publications for centuries.

@David: I can't say that I've ever noticed them in print images, but are you sure the ones you see aren't an artifact of the inks mixing at the border?

Actually my comment is not quite right. In high quality printed images a smooth interface between two inks of different colours occurs because the individual dots of ink are so small. On a computer screen there is a limit (traditionally 72 dots per inch, now generally 120 dpi or higher, but still enough to give a visible jagged edge between two adjacent colours. This is called aliasing. Computer programs can trick the eye into seeing a smooth edge  by making a transition between the colours of the pixels at the interface — anti-aliasing. cont.

cont. Looking closely at the example and generating one of my own in Photoshop with the same colours I notice that the anti-aliasing in the example is different from that produced automatically by Photoshop in having darker colours at the interface. As you say, it must have been produced by the program that generated the image, although quite why I am not sure. Perhaps a compression effect. Highly compressed jpegs can do this, although the image is currently in png format. I could add a composite illustration to your answer if you don't object.

cont. Got it wrong again. It's not a jpeg compression artifact, which is different, but a sharpening artifact. It's the way that Photoshop's "unsharp mask" filter produces its effect. I can reproduce its generation in a series of images. So as far as I can see the question is concerned, the poster is seeing what is actually there, so it is not an optical illusion. The general area of how these image manipulations trick the brain is interesting enough, but not particularly new or subject to detailed biological analysis. They just know how to do it.


text:
Apply Shannon-Weiner index to evaluate single-cell sample balance?
I would like to identify single-cell clusters where each sample is evenly represented in it. Is it OK to calculate the Shannon-Weiner index from the sample counting data of each cluster? I am worrying that the entire population of each sample is not balanced, therefore I plan to normalize within-cluster counts with total cell number in each cluster.
My naive idea is summarized in these formulas:
$$
E_{i} = \frac{\sum_{j=1}^{N_{sample\,}}P_{i,j}\log_2{P_{i,j}}}{E_{max}}
$$
where,
$$
P_{i,j} = \frac{C_{i,j}}{\sum_{i=1}^{N_{cluster}}} + pseudo\_count
$$
$C_{i,j}$ is the count of sample $j$ in cluster $i$.

What is the purpose of the pseudocount?

Pseudocount aside, you are proposing to estimate a rescaled Shannon entropy onto $[0,1]$ of each cluster. That is fine if that is what you want to know.

@Galen Log2P_ij  undefined if C_ij equals to zero. That is the cluster does not have any instances of the sample. Are there other approaches to avoid this?

That's quite understandable, however by convention we take the right-limiting value $H(0) \triangleq \lim_{p \rightarrow 0^+} p \log_2(p) = 0$.


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Which genetic oscillator should I use to generate oscillations in range of 2-20 mins?
I'm looking to phase-separate the expression of two enzymes and hence am looking for a multi-component genetic oscillator. However, repressilators and metabolators have a large period of around 45 mins. Smolen oscillators as described in Stricker et al 2008 A fast, robust and tunable synthetic gene oscillator  seem like something I could use, however, I'm not sure if I should, I am new to oscillators.
Please let me know what kind of oscillator you would recommend for a 2-20 min period time, preferably robust. Any other relevant information or recommendations are welcome. The intended system is Synechocystsis 6803 but initial work may be done in E coli.

I believe that what you are aiming to do is not possible with the mechanisms that you propose.
In most transcriptional and translational genetic circuits, the limiting factor for switching state is dilution or decay rate.
This is because genetic regulatory networks directly control rate of production, rather than concentration.  Thus, even if your oscillator instantaneously switches on and off (which it won't), your ability to turn off an enzyme depends on the rate at which its concentration decreases.
Degradation mechanisms in the cell do not operate at the time scales that you're looking for (see, for example [1],[2]), so you need to depend on dilution. E. coli at full stretch goes at about at 20 minute division time, and even the fastest doubling organisms (e.g., V. naturiegens) max out at around 7-10 minute doubling time. That gives you a half-life, not complete removal, so if you want an enzyme to be mostly off (not just decreased some), then your target times are simply not achievable with genetic regulation.
When cells need to regulate protein activity on these tighter time scales, they generally regulate protein state rather than protein concentration. This is more difficult, but if you really need to hit such tight times, I recommend that you look into such mechanisms. Alternately, do you really need to modulate this quickly?

I see. I understand the limitation my approach has. Thank you for your detailed answer. I'm actually not sure what period we're looking for, will have to check that out through mathematical modelling. I'll look into what you mentioned.
Enzyme 1's product (P) has a feedback inhibition effect on Enzyme 2, and we want to separate their concentrations in time. Are oscillators a good approach or would placing Enzyme 2 under transcriptional control of a P sensitive transcription factor? Any other approaches you can think of?

Oscillators is a very interesting idea, if you can afford a longer time-scale. Available oscillators are fragile, though, so doing that would likely entail significant focus on the oscillator. You could also use transcriptional control or try to do spatial separation (e.g., two separate strains) if the product can be exported.


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Which genes/proteins constitute the core components of the circadian clock?
What the title says.
For instance in Drosophila melanogaster and Mus musculus (see Patke et al. 2020) the CLOCK, CYCLE/BMAL, CRYPTOCHROME, PERIOD setup seems to be conserved. But other components also appear to be orthologs, and can be considered conserved (e.g., VRILLE from D. melanogaster and NFIL3 from M. musculus).
So in this case, what constitutes the "core" clock?

What do you mean by "the core clock"? Perhaps researching non-genetic evidence for circadian clocks might help.

Most eukaryotic circadian clocks--as far as I know--consist of interlocking transcriptional-translational feedback loops (TTFLs) and some adjacent machinery. All of this taken together would typically comprise of a number of genes and gene products. Some of these genes are conserved across eukaryota (as an example) and some aren't. My question basically resolves to which of the conserved genes (and which non-conserved genes, if any) would constitute the "beating heart" of the circadian clock in that this would represent the bare minimum necessary to be called a circadian clock.

Apologies for this being long-winded, @Armand.

And what makes you assume such a common core exists? Nature, unfortunately, doesn’t always play according to our rules.

I'm not assuming there is such a "core". That was precisely my question: whether or not some subset of the transcription factors and whatnot involved in the various circadian clocks across species could be considered to constitute a "core" based on persistent involvement in the clock despite speciation and other evolutionary processes. Once again, I apologize for framing my question poorly.


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How does the negative charge on endothelium prevent blood coagulation?
I was reading about the factors that keep the blood inside the body in fluid state and came across a line in my book which states that, "Smoothness of the endothelium, its negative charge and its normal health are among the important factors"
Does the vascular endothelium have negative charge on it, and if it does, how does it prevent coagulation of blood or keep it in fluid state?


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Why is this giant water bug out of the water?
I recently took a picture of a giant water bug actually out of the water.

Every instance that I have seen these of critters they have always been in the water (sometimes even feasting on frogs), but this one had climbed up onto a reed.
This could be totally normal behaviour, but it also occurred to me that there are pathogens such as Ophiocordyceps unilateralis that change insect behaviour, including climbing up blades of grass.
Is climbing up onto reeds a 'normal' or 'aberrant' behaviour for giant water bugs?

This observation was identified on iNaturalist to be an American giant water bug.

I couldn't find a definitive answer, just a suggestion that they fly to find other ponds and lakes: http://www.naturenorth.com/summer/bug/Giant_Water_Bug.html


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Why log pathogen reduction for pasteurization validation and not absolute counts?
I notice that most guidelines for heat treatment processes such as pasteurization or sterilization use a "x-log pathogen reduction" target for validating the success of such processes. e.g. For pasteurization typically the US-FDA mentions 5-log pathogen reduction.
For sterilization I often see a 9-log pathogen reduction target.
My question is: both of these are relative / ratio targets. From a product point of view wouldn't some sort of absolute target on the amount of pathogens (count) make sense?
i.e. If I have a feed which is "unclean" (has a high pathogen count) wouldn't it be easier to demonstrate a certain log reduction? Isn't this metric penalizing "clean" feeds in a sense?

I suspect it has something to do with a given counting method varying in efficiency between implementations. You may not know if a given counter reports 1 in 10 pathogen cells or 1 in 1000 pathogen cells, but that fraction shouldn't vary much over multiple counts and so count ratios should be comparable from machine to machine.

Why log pathogen reduction for pasteurization validation and not absolute counts? From a product point of view wouldn't some sort of absolute target on the amount of pathogens (count) make sense?

Because pasteurization is a manufacturing processes, not a product, it makes sense to define this process in terms of what it achieves. Namely, reducing pathogens. There may be a number of different ways to accomplish this task, and such a process may be used on a number of different products or batches of product with varying pathogen loads. A definition like this helps by providing an objective benchmark for manufacturers as well as inspectors, and often provide criteria for the specific types of organisms which should be reduced in by these processes.

If I have a feed which is "unclean" (has a high pathogen count) wouldn't it be easier to demonstrate a certain log reduction? Isn't this metric penalizing "clean" feeds in a sense?

Using a validated process during manufacturing does not excuse a producer from performing additional testing on finished products when such quality standards are in place. It essentially adds and additional layer of protection to help improve product safety. Absolute counts are often used in quality standards for finished products, in addition to pasteurization process requirements. For example, quality standards for milk, as laid out in the Pasteurized Milk Ordinance (PMO), define the numbers of total bacteria, coliform bacteria, and somatic cells (per milliliter) which may be present in "Grade A" pasteurized milk. But, these methods don't require the organisms present to be specifically identified. So, theoretically a product could contain a relatively high concentration of a single pathogen, but still meet the quality standard based on absolute counts alone. Since certain pathogens of public health concern can be found in unpasteurized milk, it remains important to use a well defined pasteurization process in addition to meeting absolute count standards.


text:
Basic clarification on definition of "unicellular"
Biology noob here, trying to expand his basic scientific knowledge.
https://en.wikipedia.org/wiki/Unicellular_organism

A unicellular organism, also known as a single-celled organism, is an
organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells.

But to me, this is ambiguous. Is a unicellular organism one that contains one cell and one cell only? Or is a unicellular organism one that contains one kind of cell, but lots of copies of that cell? So for example, are plants not unicellular because they contains groups of different types of cell, or are plants not unicellular simply because plants contain more than one cell?

Why the downvote?

The definition in the question seems to clearly (to me) refer to unicellular as a single cell only. The second half of the definition states "unlike a multicellular organism that consists of multiple cells", which seems to exclude any organism composed of two or more cells (regardless of what "type" the cells are)

Ok, so a unicellular organism is a single cell that can survive on it's own (under the right conditions). Is this what the definition means?

A unicellular organism is one where a single individual can survive all by itself under the right conditions. Some unicellular organisms live in colonies with many others of the same type or other types, and survive better in cooperation with the others (e.g. in biofilms)  but each individual there has the potential to be independent.
Multicellular organisms need more cells to survive (how many I don't know, likley organism specific).

Another way to think about it is if you take one cell, is that a recognizable organism, or is it just a part of an organism? Just to confuse things, there are certain organisms that seem to be a bit of both, like the slime molds. From wiki, "Slime mold or slime mould is an informal name given to several kinds of unrelated eukaryotic organisms that can live freely as single cells, but can aggregate together to form multicellular reproductive structures."

a unicellular organism is a single-celled organism that can conduct all the functions needed to survive on its own, in one cell. whereas multicellular organisms have different kinds of cells for different functions.
in the plant example, the plant is multicellular because it has different cells performing different functions, for example palisade cells are mainly responsible for photosynthesis while spongy cells are mainly for gas exchange.
keeping that in mind, there can always be exceptions in multicellular organisms where some are able to survive as single-celled organisms
hope this cleared stuff up.

A unicellular organism is an organism that is one cell.

I don't have any particular issues with this but answer, but it would help a bit to have citations, references, etc. It also doesn't really add much on top of existing answers.

Concise answers that fully answer the question are better than verbose ones that add nothing extra.


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Ways to predict the preservation of functional domains in fusion proteins
My lab is synthetically creating fusion proteins consisting of an enzyme attached to a zinc finger through a linker. We can attach the zinc finger to the enzyme at either its N-terminus or its C-terminus, but are unsure how to decide which terminus order to use. Have there been any attempts to predict the preservation of proteins' functional domains when they are combined into fusion proteins or, more specifically, to assess the relative qualities of different fusion protein orderings?

Naively I would think that if either domain binds with/interacts with large molecules in the cytosol, it might be better to place that downstream to minimize any effect on translation. Why not just try it both ways and see what happens in terms of synthesis yield and functionality?

A quick non-specialized search for "fusion protein zinc finger" brings up several papers dating back over 20 years. Have you looked at these papers to see where the fusions were made and whether the DNA binding activity was maintained? It would seem more appropriate to consider experience rather than prediction. And please note that you are expected to do your "homework" before posting here and to indicate in a post that you have done so and what you have found. (And, personally, I find it strange that any lab funded to undertake such studies is not aware of previous work.)


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Why is it often assumed that biological samples from mice follow the normal distribution?
I am analysing Western blot data. In the experiment, I am looking at the expression level of a certain protein of interest in the brains of wild-type and knockout mice. I have seen online that many biological measurements, especially from animals such as mice, are assumed to follow a normal distribution (and thus hypothesis tests such as t-tests and ANOVA can be applied). I have used a t-test to analyse my data, however, I was wondering why is it that measurements from mice are assumed to follow a normal distribution? Any insights are appreciated.

Does this answer your question? Do biological phenomena follow Gaussian statistics?

Many biologists (and reviewers) seem to lack a fundamental understanding of statistical testing. For me, it usually comes down to normality testing, and sample size. If I'm working with particularly small sample sizes, I'll often stick with non-parametric testing regardless of normality (and I don't think it's uncommon to see non-parametric tests in such reports). Second, I always test for normality prior to reporting a parametric test with normality assumptions. Along with any data transformations, normality testing should be reported in a paper's methods, but may not always be.

The normal distribution is often used as a "default" distribution because it is in fact quite common in measurements overall. And indeed, whenever there are a bunch of small additive errors in a measurement, the central limit theorem leads us to expect that the distribution will approximate a normal distribution. This is not a safe assumption to make, however, because there are also many cases where the error is not dominated by small additive factors.
Indeed, gene expression is one of the phenomena that are definitely not normally distributed at the single-cell level! Instead, strong genetic expression should be expected to show a log-normal distribution, due to the multiplicative factors in the chemical rates involved. Low levels of expression tend to have a Gamma distribution instead.  If there is feedback regulating the expression levels, of course, all bets are off, and even more so if you are considering a population-level measure rather than measures at the single cell level.
What typically will still have a normal distribution, however, is the error induced by an instrument as part of the measurement process (not the biological part of the assay, just the physical, e.g., measuring the intensity of a light shined through a sample). So if you assume a normal distribution, you are essentially placing a bet that the variation in your measurement process is higher than the biological variation. From my experiences with animal studies, I would say that this is rarely a safe bet to place.


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Can DNA barcoding be employed to determine the order of an unidentified haematophagous parasite?
Given: a specimen of an unidentified, highly adapted, haematophagous parasite, perhaps a species nova, contaminated with mammal blood and tissue.
DNA barcoding is readily used to identify cryptic species complexes and superspecies, in diet analysis and for food safety.
However, can DNA barcoding also be employed in a broader sense, up the taxonomic ladder, simply to identify the insect order of a parasitic specimen contaminated with mammal host material?

Yes--this is possible and has been done, e.g.:

DNA barcoding identifies Eimeria species and contributes to the phylogenetics
of coccidian parasites (Eimeriorina, Apicomplexa, Alveolata) (doi: 10.1016/j.ijpara.2011.03.007)
Developing an Apicomplexan DNA Barcoding System to Detect Blood Parasites of Small Coral Reef Fishes (doi: 10.1645/16-93)
DNA barcoding and molecular identification of field-collected Culicoides larvae in the Niayes area of Senegal (doi: 10.1186/s13071-018-3176-y)

There's also a review on the subject:

DNA barcoding of parasites and invertebrate disease vectors: what you don't know can hurt you (doi: 10.1016/j.pt.2003.09.015)


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Is there any chance that the COVID-19 virus could become more deadly by it interacting with the HIV virus?
I would like to know if there is any chance that the COVID-19 virus, or one of its variants, could become more deadly by interacting with the HIV virus.
Let's say for example, that a person who has the HIV virus contracts the original COVID-19 virus or one of its variants. When the two viruses come in contact with one another within that person's body, is there any possibility that a hybrid virus could be created from this interaction, perhaps a new variant of the HIV virus which can be transmitted by airborne transmission, or a new variant of the COVID-19 virus that can cause HIV-like symptoms in addition to its base symptoms?
I am not a biologist nor a virologist and I admit to knowing very little about virology so I am asking this simply out of scientific curiosity.
Is there any chance that the COVID-19 virus could become more deadly by it interacting with the HIV virus?

No. While both are RNA viruses, they are not related beyond that - SARS-CoV-2 is a coronavirus, while HIV is a retrovirus. They are tropic for entirely different cell types, so the chances of co-infection are low. They also replicate in entirely different ways, further reducing the chances of "gene-mixing".

Viruses are highly specialised to infect particular cell types - HIV and Covid infect totally different cell types so this seems highly unlikely.

While some viruses, such as influenza, can indeed hybridize to form different strains, you should not worry about SARS-CoV-2 hybridizing with anything but another coronavirus.  They are simply too far removed, taxonomically, for such an interaction to be plausible.
Consider the following:

The taxonomic classification of SARS-CoV-2 is: Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; Sarbecovirus
The taxonomic classification of HIV is: Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes; Ortervirales; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group; unclassified Primate lentivirus group

Notice that there is nothing in common after Riboviria, i.e., they are both RNA viruses, but have nothing else in common.
In terms of relationship, this is a branch at the same level as between us and fungi. So you should worry about HIV/COVID hybrids at about the same level that you should worry about tiger/cobra hybrids (i.e., not at all).

This is correct, but I don't think it directly answers the question - at least not mechanistically. These viruses infect different tissues, their genomes are structured in different ways, their replication cycle is different - these are the factors that decide whether genes of the two viruses cannot be packaged in the same virion. And, if they did happen in the same virion, there are reasons why they wouldn't work together.

@RogerVadim Please feel free to add a further answer if you like. I stayed at the higher level because all of the sorts of effects you're talking about are what you'd expect from divergent taxa.

actually, I was suggesting that you develop your answer. But, if I have time, I could try to do it as well


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How does medicine work?
Take aromatase inhibitors for example. In order for a molecule to stop the enzyme aromatase from converting androgens into estrogens, it must meet 6 criteria:

Not get broken down by the acidity or enzymes in the stomach (or get broken down in a helpful way)

Not get recognized as waste by the body and be absorbed through the small intestine

Not get broken down by the liver (or get broken down in a helpful way)

Get inside the cells that produce aromatase, via diffusion through the cell membrane or through a protein

Stop the production or inhibit the performance of aromatase

Not stop the production or inhibit performance of another enzyme

Despite all these criteria, multiple aromatase inhibitors exist. How did scientist find a molecule that meet all the criteria? What in biology and chemistry are they taking into account?

Pharmaceutical and chemical companies have libraries of millions of compounds that they can test using ultra-high-throughput screening with biochemical and biophysical assays. A lot can also be inferred just using structure alone, as well.


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How do I cover Cellstrainers?
I‘m doing some experiments for my bachelors thesis and I‘m using some Cell strainers by Roth for it (https://www.carlroth.com/com/en/accessories/cell-strainer-easystrainer™/p/cly9.1). My problem is that the setup is supposed to stay in an incubator at 37 °C for up to 3 weeks and it needs to be covered the entire time. Sadly I didn‘t find a proper way to cover the cell strainers which sit on top of a regular 50 mL Falcon tube. Does anyone of you have an idea or can speak from experience?
P.S.: Parafilm doesn‘t work since it gets sticky at those temperatures.

What about just setting the cap of the 50 mL tube on top of the strainer? It'll still allow some airflow, but should protect against contamination settling into it.

@MattDMo I‘m affraid the pbs solution inside the Falcon tube would evaporate. Air flow isn’t important to me since I just misuse the cellstrainer as a sample holder for a nanocomposite hydrogel I synthesized. But you just gave me an idea that might just work out. Thanks a lot!!


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Viral vector vaccines - why doesn't the viral vector get attacked by the innate immune system?
I've been looking at how the Astrazeneca Covid-19 vaccine works:
A chimpanzee adenovirus (the viral vector) is injected into the patient.
After entering a cell, the viral DNA is deposited in the host cell nucleus.

The viral DNA only contains information about the SARS-CoV-2 spike
protein.
The viral DNA does not integrate with the host cell DNA.

mRNA is transcribed from the viral DNA, and this mRNA is translated into the SARS-CoV-2 spike protein.
This is displayed on the surface of the cell where it is recognised as an intruder by the immune system which then begins producing antibodies.
Pre-existing immunity is recognised as a potential problem. From Medical News Today - COVID-19: How do viral vector vaccines work?:

With all viral vectors, one issue to consider is pre-existing immunity.
If a person encountered the virus that serves as the vector in the past, they may have antibodies to the virus. This means that their body will try to fight and destroy the viral vector, potentially making a vaccine less effective.

But where is the innate immune system in all this? My (layman's) understanding is that the very fact that the virus particle was novel would result in an immediate response from the innate immune system. How does the viral vector get past it?

These Chimpanzee adenoviral vectors do not bypass the innate immune system at all. In fact they are used precisely because of their activation of the innate immune system, which then results in greater immunity because activation of the innate immune system results in antigen presentation and then activation of the adaptive immune system.
The reason they activate the innate immune system is because these viruses do not have a seroprevalence, so they can only activate the innate immune response with an end result of antigen presentation. In contrast, human adenovirus vectors generally have a high seroprevalence (because we've all had colds caused by adenoviruses), so they activate the adaptive immune response against the viral particle (vector), clearing it before presentation of the novel antigen (in this case the CoV spike protein) can occur.
There's a nice commentary on the different mechanisms by which the ChAdOx1 (Astrazenica/Oxford) and the mRNA (Moderna/Pfizer) vaccines work at Nature Reviews Immunology. To quote the relevant paragraph (emphasis mine):

The AdV vaccines also contain inherent adjuvant properties, although these reside with the virus particle that encases the DNA encoding the immunogen. Following injection, AdV particles target innate immune cells like DCs and macrophages and stimulate innate immune responses by engaging multiple pattern-recognition receptors including those that bind dsDNA — in particular TLR9 — to induce type I interferon secretion8. Unlike AdV vectors, mRNA vaccines do not engage TLR9, but both vaccine formulations converge on the production of type I interferon (Fig. 1). Type I interferon-producing DCs and other cells that have taken up the vaccine-derived nucleic acids encoding the S protein can deliver both an antigenic and inflammatory signal to T cells in LNs draining the injection site. This activates S protein-specific T cells and mobilizes adaptive immunity against SARS-CoV-2

One of the problems with using a simian adenovirus vector like the ChAdOx1 vector is that now a large portion of the population will have some antibody response to the vector (as well as the introduced spike), so future uses of this same vector might not result in as high an immune response as we have seen this time around, when the population is almost entirely naive.

I believe that if you read carefully, you'll see that your answer and mine are consistent with one another.

@jakebeal - sorry, I misread your post- I interpreted it to say that the innate system is suppressed and by implication the adaptive is used because of your second sentence. I've edited my post to suit.

@bob1 Re "One of the problems with using a simian adenovirus vector like the ChAdOx1 vector is that now a large portion of the population will have some antibody response to the vector (as well as the introduced spike)". What stimulates the antibody response to the vector? Is it "the adenovirus's foreign proteins" as mentioned by Jake Beale?

@Naj exactly. Just the same as if you had an infection with the adenovirus.

@bob1 OK. Finally, do these "foreign proteins" present themselves on the surface of the infected host cell along with the spike protein? Thank you for your patience!

@Naj I think you need to review how the system works, with the correct information, it should tell you how the vaccine works and how the body responds to foreign proteins in the context of infection.

@bob1 - will do :)

The innate immune system has many different components to it. If we consider a natural virus, like the base adenovirus used as a vector used in the Oxford/AstraZeneca vaccine, then we can assume that the virus already has sufficiently effective strategies in place to deal with them.
In particular:

Physical and chemical barriers are irrelevant, given an injected vaccine.
Interferon and MHC pathways must already be either ineffective or slow enough to be secondary in the response against the adenovirus's foreign proteins, such that NK cells shouldn't be expected to change their efficacy.
The vaccine protein isn't expected to damage the cell membrane, so that pathway won't change either.
Inflammation and antibacterial pathways aren't triggered by presentation of an extra protein either.
Activation of the adaptive immune system through antigen presentation is exactly the sort of response that is desired.


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Please help identify the species of a possible butterfly
I took picture of this weird butterfly. It landed when I was drying my clothes. But it didn't even move when I try to shake it off. After I took a lot of pictures, I tried to shake it outside.
It might not be clear in the picture, but there is a bit of pink on its 2 wings near the body in the next to last picture.
Location: Asia (Southern part, Vietnam), and this butterfly is in the countryside.
Climate: hot, humid, it is currently Raining season, night is cool, day time is not too hot.
This might even be a type of moth?

Definitely a moth, probably hawkmoth. Very beautiful

Please [edit] your post to include an estimate of the size of this insect — that information can be very helpful for identifications. Also, are mango's grown nearby — adding that information is now very relevant given bob1's answer.

I googled the name, and yes it match up perfectly. I released the moth already, so can't put it with a ruler, but it is around the palm of your hand. Yes, there are plenty of mango trees around my place, sorry I didn't think about adding the surrounding tree type for better reference.

I'm no expert - just like browsing pictures, so totally open to other suggestions.
I think this is the Mango Hawkmoth/Sphinx moth (Amplypterus panopus), which is a fairly widespread moth of SE Asia, including Vietnam and Thailand.
You can see the pink of the underwings (terminology?) here and you can see the big lines across the wings. If you imagine the wings folded so that they lie across the body, you can see the nice horizontal stripes and dark head seen in your photos.


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What is the botanical definition of a tree?
I recently saw a shared post on Facebook which states

Trees - even a young child knows what a Tree is, however there is surprisingly no universally recognised precise definition of what a tree is, either botanically or in common language. In its broadest sense, a tree is any plant with the general form of an elongated stem, or trunk.

Wikipedia points out (without citations)

In botany, a tree is a perennial plant with an elongated stem, or trunk, supporting branches and leaves in most species. In some usages, the definition of a tree may be narrower, including only wood plants with secondary growth, plants that are usable as lumber or plants above a specified height. In wider definitions, the taller palms, tree ferns, bananas, and bamboos are also trees. Trees are not a taxonomic group but include a variety of plant species that have independently evolved a trunk and branches as a way to tower above other plants to compete for sunlight.

I always considered palm trees and banana trees to be trees. Is it true that botanically, they are not trees? What is the true botanical definition of a tree?

Here is a reference that might suffice to convince you that there is no "true botanical definition of a tree": https://silvafennica.fi/article/463 And since I like to nitpick occasionally: A definition is not something that can be true or untrue. At most, a definition can be common and accepted, possibly even endorsed by a scientific society or codified in regulations or laws.

You will find for many biological concepts they don't bother trying to use or recreate vague lay concepts. You will also find biological definiens are often not hard and fast because life exists in a continuum.

According to "Plant Identification Terminology: An Illustrated Glossary" (Harris & Harris, 2001):

Tree: a large woody plant, usually with a single main stem or trunk.

An emphasis here should be on the woody characteristic. I'm not sure many botanists (if any) would define 'trees' without woodiness being part of the definition. As such, botanically speaking, the growth habit of neither bananas nor bamboo would be considered a tree.
The variation between tree and shrub is much less well-defined, and no "standard" definition exists. Often times, the number of stems coming from the base is used to differentiate trees (one or few stems) from bushes (many stems), but this is not universally applied or useful.
Emphasis here is "usefulness". Differentiating shrubs from trees is honestly arbitrary and typically dictated by the application to which the definitions are being applied. In many cases, simply differentiating by maximum or average growth size can serve as the differing characteristic as size is going to often be most relevant for landscaping (i.e., trying to achieve desired sizes) and ecological applications (i.e., which part of the community strata the tree reaches in terms of light availability). Often, botanical studies will explicitly indicate their definitions of tree vs shrub by indicating a cutoff or transition height tat they use to differentiate the two. However, in many studies, both would be considered relevant and a "cutoff" would be unnecessary.

In other words, number of stems and maximum growth can and are often used to differentiate trees from shrubs, but no standard number of stems or specific growth size are universally used to differentiate both woody growth habits.


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Can anyone identify this fish?
I saw it in the sea very close to the beach in front of Starfish Hotel in St Lucia. It had some spines along its back and it seemingly had fins on each side that split open into 4. It used its front two fins to dig through the sand. It had white spots, and the main colour of it was very dark brown - black. The fins on the fish were very thin and flimsy-looking.
From tail to head was probably around a foot long, and the end of one fin to another was around 15-20 cm.
Here is a link to a video I took seeing as the picture may not be clear enough- https://drive.google.com/file/d/1PzjgzAaK6B51jg9HHNO4SQyorepsdKLB/view?usp=sharing

Welcome to Biology.SE! It will improve your chances of getting an answer if you include an estimate of the size of the organism. Clearer photos would also be very helpful, but I understand that may not be possible. Please [edit] your post to include this essential information. (For future reference, identification questions should always be given the species-identification tag.) ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. Thanks!

The array of fins brings Lionfish to mind, bit I have no idea if this is what they look like from above.

@bob1 I just looked up images of them from above. It doesn't look like it, if you ask me. It almost has a pufferfish-like body.
https://media.sciencephoto.com/image/c0153618/800wm/C0153618-Lionfish_from_below.jpg

Yeah, and I haven't been able to find a list of fish species with pictures from the area either... lots of sport fishing species, but nothing for the in-shore or estuarine.

Based on the location, size, behavior, and shape (particularly of the pectoral fins) this appears to be a flying (or helmet) gurnard (Dactylopterus volitans) with its "wings" folded.
These range of these fish includes the Caribbean and they are known to use the forepart of their pectoral fins (i.e. the free extra 'fin' near their head) for "exploring the bottom" 1-3, which fits the behavior you described.
The size is also reasonable since they are said to reach up to 50 cm in length.
Image below for comparison — note these fish are described as being highly variable in coloration.

Image © slebris from iNaturalist some rights reserved
References:

https://fishbase.mnhn.fr/summary/1021

Roux C; Dactylopteridae. In: Miller, P. J., Whitehead, P. J. P., Bauchot, M. L., Hureau, J. C., Nielsen, J., & Tortonese, E. (1986). Fishes of the North-eastern Atlantic and the Mediterranean. Vol. III. Richard Clay Ltd, Bungay, United Kingdom.

Davenport, J., & Wirtz, P. (2019). Digging with ‘hands’: observations of food capture in the flying gurnard Dactylopterus volitans (Linnaeus, 1758). Journal of Natural History, 53(41-42), 2489-2501.

Excellent choice, It didn't even cross my mind that gurnard would be present there.

@bob1 —— Thanks — gurnards do have a surprisingly wide range. I actually stumbled on this while I was researching a comment suggesting the OP look on iNaturalist since they clearly weren't going to get an answer here!