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How were the first genes isolated from genomic or cDNA libraries without already knowing a hybridization probe?
Let us go back in time to around 1975. It is my understanding that at that point (or at least by the end of the decade), both genomic and cDNA libraries had been created for a few organisms, e.g. rabbits. I'm interested in the logic of techniques that first used these libraries to isolate genes encoding for particular proteins. Note: I'm not interested in how we'd isolate a gene today; I want to understand the history.
First, consider the following thought experiment. Say it's around 1975. The one assignment for my Cal Tech biology class is a doozy: it goes as follows. The instructor (Tom Maniastis?) hands me a protein along with the cells from which the protein was isolated as well as genomic and cDNA libraries of the organism that makes the protein; the challenge is to isolate the gene encoding for the protein. I do not know anything about the protein except that the product I've been given is pure.
Of course, the basic idea is simple: isolate the gene by screening the libraries with a radioactive nucleic acid probe and using a hybridization assay. But alas, I do not have a complementary probe: all I have is the protein! What do I do?
Here is one solution I can imagine. (I don't know whether it was possible around 1975, much less whether it actually happened.) I could try to isolate the mRNA that codes for my protein (but how to do that?), then radiolabel it and use the radiolabelled mRNA as a probe in a hybridization assay on the cDNA library (not the genomic library, since the unprocessed DNA could have noncoding regions).

Would this have worked?
Did anyone actually do this?
If yes to either (1) or (2), how could one figure out which mRNA coded for the protein?

The question, in essence, is how to get to DNA, given only a protein, circa 1975.

I am curious as to why you posted here. If you really are at Caltech and just wanted to know the answer you should be smart enough to do a literature search and find the answer. However, again if you are at Caltech you presumably are bright enough to want to work it out by yourself, so you don't want those of us (me) who were around in 1975 gave you the answer (which I won't). As you, yourself admit, your proposal is flawed ("how to isolate the mRNA?"). Do you want a hint or discussion? That's not what SE Biology is for. Tell me why I shouldn't vote to close.

@David: I'm not at Cal Tech. I'm a math-trained grad student in the history and philosophy of science. I said explicitly it's a thought experiment. I don't know how to find the result in the literature. If you want a different way of asking the question: tell me how Maniatis et al 76 and 78 got mRNA rabbit insulin probes. I'm not trying to start a discussion: I want the answer. I find it cynical and unnecessary for you to assume I didn't want the answer.

Another possible solution: get the protein's amino acid sequence (using Sanger's technique), then synthesize a lot of RNA or DNA probes compatible with it (there will be a huge number, thanks to degeneracy of the genetic code). But was synthesis possible then? I don't know enough of the history to know which of these methods could've been done in the late 70s.

I wasn't being synical, just trying to find the context to your question (which nobody else had responded to). Your latest suggestion is a more logical use of the pure protein idea. You might think what else you can do with a pure protein, and also — as you mentioned cells — why proteins like insulin and globin were "low-hanging fruit". I'm a bit busy at the moment, but will respond in due course if nobody else does.

Thanks. I assume no one answered because others don't know the answer: it's a non-trivial problem, not Googleable or capable of being looked up easily. I know insulin and globin were overproduced by insulinomas and red blood cells, so their mRNAs were abundant. But how to isolate the mRNA responsible for insulin, say, in particular?

This paper seems to be the first to isolate the rat insulin gene. I'll convert it to an answer later if I find the time.

Many genes responsible for a given phenotype were discovered by forward screens using marked transposons or complementation mapping. I could also imagine a scenario where the protein sequence is used to create a degenerate oligonucleotide to probe a cDNA or gDNA library.

@canadianer: thanks for your comments. I don't know what "forward screens using marked transposons" and "complementation mapping" are. maybe I could google them, but a succinct high-level description of the idea could work nicely as an answer. I'll read the Ullrich et al rat paper in the meantime.

The key sentence in the Ullrich paper is on the second page: "It seemed likely that the Hae III fragments were derived from insulin cDNA because of their prominence in the total cDNA preparation." So the answer to my question is that researchers exploited the overproduction of insulin in B cells to harvest all the mRNA, reverse transcriptase to cDNA, restriction digest, and then make an educated guess that the most prominent fragments contained the insulin gene, due to the high expression of insulin.

You can read this Wikipedia page for a start. In this case you don't start with a particular protein of interest but rather randomly mutate the genome and look for altered phenotypes. Then you look for the mutation that caused the new phenotype. If you used transposons for mutagenesis, you can include some kind of marker that allows you to quickly identify clones containing the mutated DNA.

@canadianer — If this question isn't taken off-topic, we should be providing proper answers. I've found a section of a book chapter I wrote last century on the topic, but it will take me time to condense it. Not before next week.

@David Agreed, I will write something soon hopefully. I look forward to your answer.

@David: can you just point me to your book chapter? Of course, you can answer here, when you get a chance, in order to close the question. But I'm very interested to hear that you wrote an entire chapter on this.

The following is based on a chapter on Cloning DNA in the 10th edition of The Biochemistry of the Nucleic Acids (RLP Adams et al.) published by Chapman & Hall in 1986. (This is probably more pertinent than the 11th and final edition, which was published in 1992 and had a more contemporary treatment.) Apologies for the fact that it will be difficult to find.  It should be available from some university libraries and through inter-library loan systems in certain countries. Section A.7.3 gives a taste of the methodology used at that time.
Protein properties that could be used as the basis of a cloning strategy
In attempting to clone DNA for a particular protein for which there were no pre-existing clones to use as hybridization probes, one had to consider the properties of the protein one is able to exploit. These might include:

Amino acid sequence
Antibodies to the protein
Biological activity
Particular physical properties, such as size

(Clearly if one had no such ‘handle’ to the protein one was not in a position to try to clone its cDNA or gene.)
Three general approaches
There seemed to be three general approaches:

No expression
Indirect expression
Direct expression

The approach that one might take was also governed by whether the protein is particularly abundant in a specific tissue, when one might expect less sophisticated more labour-intensive approaches to stand a chance of success.
Another point to emphasize is that, at least with eukaryotes, one would look for a cDNA clone first, and only try for a genomic clone after one had this to employ as a hybridization probe.
1. ‘No expression’ approaches
In the no expression approaches one relied on the amino acid sequence to identify the cloned DNA. One such approach was to use hybridization probes against stretches of amino acids, the codons of which had limited redundancy (Met and Trp have a single codon, and some other amino acids only two) using low stringency hybridization conditions. This required luck. Alternatively one could sequence random clones and hope to find one that correlated with the amino acid sequence. At that time DNA sequencing was slow and labour intensive, so that this was only applicable to proteins that were relatively abundant in the tissue from which the libarary was prepared.
2. Direct expression approaches
Direct expression generally entailed using a bacterial expression vector which produced a fusion of a bacterial protein with a part of the eukaryotic protein. (Statistically only one in six of clones would have the correct reading frame in a fusion protein.). This approach was favoured if one had an antibody, which did not require a complete protein.
3. Indirect expression approaches
By indirect expression was meant using immobilized cloned cDNA to select corresponding mRNAs (‘hybrid selection’) which could be expressed in a cell-free system. This was appropriate if the distinguishing characteristic required a full-length protein, as in the case of biological activity or size.

Specific to the insulin gene, the following paper is, as far as I can tell, the first to isolate it:
Ullrich A, Shine J, Chirgwin J, Pictet R, Tischer E, Rutter WJ, Goodman HM. 1977. Rat insulin genes: construction of plasmids containing the coding sequences. Science 196:1313-1319.
The took advantage of the fact that insulin is produced by β cells in the pancreas and so are enriched in insulin mRNA. After poly(A) RNA was isolated and reverse transcribed, the major band observed upon electrophoresis of the resulting cDNA was expected to belong to the insulin gene:

It seemed likely that the [major] fragments were derived from insulin cDNA because of their prominence in the total cDNA preparation. Therefore, these fragments as well as the complete cDNA preparations were used in the cloning experiments.

Thus they cloned this cDNA, sequenced it and discovered that it contained the entire proinsulin coding sequence:

Since the mRNA contains a terminal poly(A) sequence, the [cloned] DNA strand containing 3' terminal poly(dA) is of the same sense. This strand determines an amino acid sequence which exactly corresponds to the entire coding region for rat proinsulin I and 13 out of 23 amino acids of the prepeptide sequence.

With this sequence determined and because of its high degree of conservation, the homologous human gene could be isolated by hybridizing with rat insulin cDNA:
Bell GI, Swain WF, Pictet R, Cordell B, Goodman HM, Rutter WJ. 1979. Nucleotide sequence of a cDNA clone encoding human preproinsulin. Nature 282:525-527.


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How many proteins are in the Earth's proteome?
Humans alone have thousands of proteins. With that in mind, it seems like the total number of proteins among all species would be very large.
Are there any available estimates for how many proteins exist on earth in all organisms? I'd also be interested in how many of these are unique proteins as opposed to proteins that are very similar to other proteins, i.e an estimate of non-redundant proteins alongside the redundant proteins.

Well, remember that just about all proteins are evolved from other, related proteins, so how many you consider unique is really a matter of definition. If you and I have a protein with a single amino acid substitution, is that a new protein? Kind of makes the question impossible to answer.

As @BryanKrause mentioned, if you intend 'unique' to signify "found only in humans/only inone of all other organisms", there will be very few. If you mean 'unique' to mean "different", we don't have that answer. We're still discovering new species almost every day!

@BryanKrause Protein redundancy is a fairly common method of allowing clusters of proteins to be represented by a single protein. This avoids biases introduced by overstudied systems or by large groups of very similar proteins masking distant proteins that would have different biochemistry. It's a scientific way of generating lists of "unique" proteins.

I see no reason it should be closed as unclear. It's a simple easy to understand the question. It's subjective indeed, but there are papers estimating these types of questions, so it's not completely a matter of opinion.

I'm voting to reopen this question since there have been scientific studies on exactly this question. See "Towards the completion of the earth's proteome" Perez-Iratxeta et al. 2007. This question can be quantified and objectively explored. On the other hand, the unclear votes appear to be from a miscommunication that single sequences can represent homologous clusters. I've edited the question to make this part of the question more clear.

To the close voters, what about this question is too broad? Potentially it could be answered with a number and a citation alone.

Current records
According to Uniprot, there are 85,381,808 protein records, and with the UniRef90 filter (i.e removing records that can be represented by an entry with at least 90% sequence similarity), there are 42,424,511. However, these databases are moving targets and will change over time. We will sequence more species, find novel splice isoforms, and various other methods will expand the databases. Indeed, the databases will be truncated also from time to time as some hypothetical proteins may be based on genes that turn out to not code for proteins after all.
In 2007, a study estimated that the earth's proteome would contain around 5 million sequences, and that the majority of these would be elucidated by 2012. I suspect this is a very thorough study, however, a lot has changed in the last 10 years. This estimate is actually less than the nearly 9 million species estimated in more recent studies.
Approximate estimate
So let's do some back of the envelope maths. Let's assume the article estimating nearly 9 million species is about right, and that we've only catalogued some 1.2 million. But UniProt isn't even close to this number.UniProt contains 25477 scientific names in it's controlled vocabulary. So for 25 thousand names, we have 85 million protein records. What if we had 8.75 million names?
Let's assume:
$\frac{Predicted~Proteins}{Predicted~Species}=\frac{Known~Proteins}{Known~Species}$
We can rearrange this to:
$\frac{Predicted~Species~\times~{Known~Proteins}}{Known~Species}= Predicted~Proteins$
Generous estimate (Uniprot, 335527 proteins per species):
$\frac{8750000\times{85381808}}{25477}=2.932413e^{+10}$
Conservative estimate (Swissprot, 41 proteins per species):
$\frac{8750000\times{554241}}{13408}=3.616952e^{+7}$
For the sake of completeness let's assume the number of <90% identical proteins will remain around half that value. We can say that there might be around $1.8e^{+7}$ to $1.5{e}^{+10}$ "unique" proteins, less than a trillion ($1e^{+12}$). Given the absurdly generous 335 thousand proteins and very stingy 41 proteins per species, we can be fairly certain that if there are indeed 8.75 million species, the number of proteins will fall between those estimates.
The biggest assumption here is that the proteins have a linear relationship with species which is unlikely to be the case, and at the generous estimate we are pretending that there are no proteins in UniProt that don't have species annotation. As for Swissprot, this only includes proteins that have been manually curated, so this ignores many proteins that are safe to assume exist and typically only covers proteins that are of interest to scientists.

A minor correction to your question, the UniProt lists ~20 thousand protein coding genes in the human proteome, not millions. Those protein coding genes are subject to various post translational modifications and isoform splicing, so there will be more final proteins than 20k.

The human proteome can contain millions of different proteins if we consider proteins with different post translational modifications (PTMs) to be different!

@JeppeNielsen I asked a similar question on this: Why does UniProt list 150,000 proteins in the human proteome?

Just because a database does not consider proteins with different PTMs to be different, does not mean that the proteins are identical. If you disregard PTMs you cannot explain the ABO bloodtypes as they are caused by differences in the glycosylation patterns.

Another good example would be the insulin receptor, which comes in many different variants.

@JeppeNielsen Yes, there are many PTMs, splice isoforms, and other variants that perform different functions. However, they are all from ~20,000 protein coding genes.

So you would say that the genome contains ~20,000 protein coding genes. The proteome is much larger.

@canadianer There isn't yet a strict definition of the proteome. UniProt has 20k records under the human proteome. After PTMs and isoform splicing, there are many more proteins. I've said this in the comments but since two people are not happy for some reason, I've edited the answer to be clearer.

Each UniProt record contains isoforms and modifications. That they choose to organize their database this way doesn't seem to me to have any bearing on the definition of the term proteome. Any definition I have heard refers to the entire complement of expressed proteins. See UniProt's, for example: A proteome is the set of protein sequences that can be derived by translation of all protein coding genes of a completely sequenced genome, including alternative products such as splice variants...

PS: I apologize if I seemed argumentative; that was not my intent. I think definitions are important but I  also realize that there aren't any real authorities on a lot of terminology.

Thank you canadianer, you previous comment highlight what I was trying to get across. Which namely is that the number of database entries is way lower than the possible number of proteins derived from those entries.

@JeppeNielsen Yes, I see your point. But even if each record had an average 10 splice and PTM isoforms, these errors are nothing compared to the other error causing assumptions that seem to generate several orders of magnitude of variance in estimation.

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What was the first known flower meant for a flying pollinator insect?
I think flower ancestors were colorless and sugarless. The first flower then chanced upon using insects by attracting them. Has this flower been discovered and from what ancestors did it evolve from?

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Can I breed the most productive hen by hatching eggs from the most productive ones?
Here is some hypothetical input:

I have a set of eggs.
I hatch these eggs and get chicken from them. Say, 100 hen that can lay eggs.
I have a hypothetical technology to track some parameters of each hen during their life - one of them is the moment a hen lays an egg.
I collect the data and find out which hen laid the largest amount of eggs during her productive period. I mark this one as the most productive.
I collect the eggs from the most productive hen in the generation.
GOTO 1.

Now, if I repeat this loop of death and life, say for 20 generations, hatching only eggs from the most productive hen, will it make next generations more productive and with each iteration or is it an oversimplified picture I have?
By performing this mental experiment I want to figure out if I can use it as a clear predictable factor influencing productivity of future generations.

In theory yes, so long as you maintain genetic variation within your flock of hens (e.g. by bringing in outsider males to prevent inherited diseases spreading), artificial selection will lead to a more productive flock.
However I don't think it would be predictable and not necessarily an improvement every generation, surely productivity would be influenced by lifespan? e.g. is it better to have a hen that lays 100 eggs/month for 24 months, or a hen that lays 120 eggs/month for 12 months? Not necessarily that important, but worth considering.
You would also want to keep more than one hen per generation, maybe 2 chick hens from each of the 3 most productive hens per generation, just in case you selected one that hadn't inherited the productivity traits.
I assume you've read about milk yields. And this looks like it covers the maths of heritability of egg production.


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Why can't dopamine cross the blood brain barrier but l-dopa can?
Levodopa can cross the BBB and is less lipid soluble then dopamine, so dopamine should be able to cross the BBB more easily then l-dopa, but for some reason dopamine cant cross the BBB. Both dl-methamphetamine and levomethamphetamine can cross the blood brain barrier, but why not dl-dopamine?

Both L-Dopa and Dopamine are polar molecules and thus hydrophilic. They are solvable in water but not in lipids, so they are not able to cross the Blood-brain barrier on their own.
The difference is that L-Dopa has a transport protein (SLC7A5) that allows it to pass through the Blood-brain barrier, whereas dopamine doesn't.

Yeah, that's LAT1, but why doesn't DAT1 have any effect?

If you look at the distribution of LAT1 versus the distribution of DAT you can see that LAT1 is distributed in the blood-brain barrier, whereas DAT is not.


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What do butterflies eat?
I found a beautiful scarce-swallowtail butterfly in my storeroom, but it was kind of frozen and couldn't fly away. So, I put it on my terrace in the sun. After a little bit, it flew a few meters away and fell. I was wondering what could these beings eat, so that I can help it...
Any answers would be great appreciated!
Thanks in advance

Nectar is one of them. Perhaps some weird species also have some unusual diets...

@YvesLaFayette It's probably done reproducing, so there's no reason for it to eat or fly any more. Sorry...

Butterflies die. :( That's probably what yours is doing. But if you have a blooming butterfly bush or any tubular flowers in bloom right now, it's worth a shot.

More probably it's dying (butterflies know how to find food by themselves), or there's a small chance your sugar concentration was too high or too low?

Be careful you don't overfeed them.

Adult butterflies don't eat! I mean.... not in the sense of chewing on food. They rather drink. They get their nutrients via ingestion of liquid substances. Their mouth consists of a long tube called a proboscis that acts as a straw.
What do butterflies feed on?
The vast majority of butterflies eat nectar from flowers. Many species are quite specialized and feed on the nectar of a few species only.
There are a few exceptions though. Some species feed on tree sap, dung, mud (see mud-puddling), pollen, or rotting fruit. Butterflies are attracted to sodium and may as well try to feed on human sweat but I doubt there exist any species would get a non-negligible source of nutrients from human sweat. Coming to exceptions, you should definitely consider reading @DmitryGrigoryev's answer as well.
What do caterpillars feed on?
Of course, you are probably aware that butterflies have a complex (-ish) life cycle. The larva is called a caterpillar, while the adult is called a butterfly. So what do caterpillars eat?
Caterpillars have mandibles, so they can chew tissues and not just drink. Most caterpillars eat leaves and other plants parts. Again, many species are specialized to only a few plant species.
There are of course exceptions. For example in the Phengaris genus, (such as the famous large blue (Phengaris arion), caterpillars live in ant colonies and mimic the larvae of these ants. Some of them are able to trick the ants into feeding them as though they were ant larvae (e.g. Phengaris alcon, Phengaris rebeli). Others (e.g. the aforementioned Phengaris arion) will act as predators and eat the real ant larvae!
When the butterflies emerge from their cocoons after metamorphosis, the ants finally figure out the trickery and start attacking the butterfly. The butterfly has therefore very little time to try to fly away from the colony before getting killed. It is a critical life stage for individuals of this species.
How to feed a butterfly?
This section exists thanks to @Rodrigo's recommendation.
As a substitute of nectar one can simply use sugar water. The optimal sugar concentration (in mass-mass) is around 35% (Kim et al. 2011) although it likely varies among species.
Kim et al. 2011 explains that what limits optimal sugar concentration for insects is the viscosity of the solution. Too much sugar renders the solution too viscous and difficult to forage on. Interestingly, the ability to drink viscous solutions depends upon the drinking technic (active suction, capillary suction or viscous dipping) which vary, not among butterflies but among insects. The article is interesting.

Then there are other metamorphic species, e.g., Luna Moth, which don't even have a mouth in their 'adult' stage.  They don't eat at all after exiting the coccoon.  Oh, never mind, Dmitry has that covered.

It would be great if you specify the limits of sugar concentration butterflies can drink on. I know the amount is different between bees and hummingbirds, but don't remember the numbers, and don't know about butterflies either.

OP, do you have a source for "When the butterflies emerge from their cocoons ... the ants finally figure out the trickery and start attacking the butterfly"? The Wikipedia article for one of the Phengaris species cites a book called "Extraordinary Animals: An Encyclopedia of Curious and Unusual Animals" in support of this, but I can't find a peer-reviewed paper or other authoritative source to back it up. Footage from the BBC's "Life on Earth" shows the butterfly leaving the nest unhindered, and there are anecdotal claims that Large Blues can even have the ants escort them outside!

@Astrid_Redfern No, sorry I don't have a peer-review reference for it. I am just repeating stories I have heard!

Several species of the order Lepidoptera don't feed at all in adult form, surviving entirely on the reserves made while they were larva. Two examples I'm aware of are the Atlas moth (as well as most of the family it belongs to) and the clothing moth.
Also, many butterflies and moths which normally do feed stop doing so after the mating (for males) or after laying all the eggs (for females). This might be the case of the butterfly you have found: if it has completed its reproductive program, it just looks for a place to pass away in peace and no amount of food and sunlight will revive it.

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Understanding PAM and BLOSUM matrices
This question might be silly but I need some clarification.
I'm slightly confused about if there are multiple PAM and BLOSUM matrices? Is there a different matrix for each sequence?
My understanding is that PAM and BLOSUM are substitution matrices that are used to demonstrate how similar a sequence is to other sequences by seeing how many iterations of the matrix multiplication are needed before being able to achieve a "similar primary composition". Is this correct?
As I've understood it this means that if I want to compare 2 sequences together I can just this iterative calculation until the relationship between my target sequence and my initial sequence is maximized and then see if that similarity is enough that I can say they are closely related.
This is all assuming there is one standard PAM250 and BLOSUM62 matrix which I'm assuming are calculated from information derived from all information collected on protein sequences.
So when using PSIBLAST to search for similar sequences using BLOSUM matrices does it calculate similarity scores using BLOSUM matrices and then if this score is above a certain threshold it returns that sequence. If you do this for multiple iterations then what is the next input that it uses?
Thanks
EDIT: I think some of the reason for my misunderstanding is that I'm not sure why there would be one single matrix which can be used to determine the "resilience" of a particular amino acid in general. Isn't the "usefulness" or that amino acid dependent on the function of the protein? In that case shouldn't there be different substitution matrices for different proteins? Is this why PAM matrices have difficulty and is this semi-solved by using BLOSUM matrices which use blocks and so can capture when certain "blocks" of amino acids correspond to particular functions and are therefore seen together a lot and are resilient to change in that way? It still seems a bit strange to lump them together in this case.

There are multiple matrices. The matrices scores various mutations slightly different and the use of them depends on how big the evolutionary distance is expected to be among the sequences.  (https://en.wikipedia.org/wiki/Point_accepted_mutation)(https://en.wikipedia.org/wiki/BLOSUM)

@JeppeNielsen There are multiple matrices as the matrix is generated based on the sequence that I'm querying? Or there are a few standard matrices that are used depending on the type of query?

Possible duplicate of Scoring matrices (BLOSUM & PAM) in BLAST and other sequence-comparison programs

Possible duplicate of https://biology.stackexchange.com/questions/49036/scoring-matrices-blosum-pam-in-blast-and-other-sequence-comparison-programs. Please search for other questions on a topic on SE Biology. BLOSUM brings up several hits.

@David Sorry, I don't think it's the same thing. I came across that topic and read it multiple times but it doesn't answer my question.

That answer only states how they're calculated not what data is used to calculate them nor does it discuss differences between matrices when using different query sequences, or intuition behind "lumping them together" which is what I'm after :/

The Wikipedia entries describe the data used for these matrices. As already commented, many pre-existing Protein (not DNA as in your question) sequences are needed and used to get a meaningful matrix. No, it isn't perfect, but your intuition is wrong — it works well enough. No, you can't use a matrix from two sequences, and especially two you are trying to align with a program that uses a matrix. Yes, you can modify standard matrices to get position-specific matrices as you perform multiple alignments of many sequences you already know are similar (see docs for Clustal).

Not at all. I don't answer questions in comments, so if others don't vote this as off-topic, I'll post a proper answer next week. (But anyone else is at liberty to spare me the chore.)


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What is the meaning of the word 'bin' in the context of RNA-Seq?
I have a question from a book about RNA-Seq. I would like to know the meaning of the word "bin" in the below cited paragraph:

RseQC has several nice features not found in the other programs: (a)
  When calculating read distribution between different genomic features,
  it reports also several bins upstream and downstream of transcripts.

It's talking about things like "TSS_up_1kb", which is a "bin" of 1kb upstream of the gene. A bin is a somewhat generic term that in this context means "a region of some given size". Another example where you might see the term is with histograms. There, values are grouped into bins, with each bin then being represented by a separate bar in the graph.


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Why are sushi proteins called "sushi"? What are the origins of this name?
Does anybody know why complement control proteins (also short consensus repeats) are called "sushi" proteins? Is there any special reason for their name?

Hi Welcome to Bio.SE. Your question could use a tad more context to demonstrate that you've tried answering this on your own. We always ask that the asker provide evidence of prior research. See here. Thanks.

People who discover things have some small reward in being able to name it whatever they want within reason. There's a moth with donald trump like hair which was named after him, and some proteins have incredible names (my current amazement is with the sonic hedgehog protein.) Sometimes - after a while - the names are changed if particularly ridiculous. Sometimes not (luciferin is a prime, imaginative example.)

@anon Biologists, in particular, like to be clever/creative with how they name things, but it has gotten them in a bit of trouble in the biomedical area. It turns out that when patients have some kind of debilitating disease, it doesn't go over particularly well when the doctor starts trying to explain to the family what causes the disease, and some protein or gene with a funny name is implicated. There have been movements to change some of the real zingers that arise most often in clinical cases, but inertia has gotten in the way (plus some resistance from those of us with a sense of humor).

@CodyGray - Yep. Am following the controversy around sonic hedgehog and personally think, out of respect for the devastating illness it is associated with, it should be changed. But I might feel differently if I were the biologist involved. In this case, though.... I would not have named it sonic.

@anon Oh, you had cited Sonic Hedgehog, but I didn't realize you already knew of the controversy surrounding it. The reason for the "Sonic", though, is that this is actually the fourth protein in a class of developmental-patterning proteins. The others are named after real species of hedgehogs: Indian hedgehog, desert hedgehog, and moonrat hedgehog. So it's not like someone just pulled the name completely out of the blue. No one ever talks about it, but I don't think those affected would feel much better telling them they had a defect in their moonrat hedgehog gene, either. :-)

@CodyGray - :) Thanks. I do understand the natural progression, but knowing the disease associated with it does (or should, imo) have some bearing on the name. For example, if there were a group of proteins called "camper proteins" that caused serious mental handicaps, I would not like to see one named happy camper, no matter how humorous that is. But, it's not in my hands, I'm glad to say.

@anongoognurse I believe the naming preceded the discovery of the diseases it caused.

Note that most (all?) of these names come from experiments in Drosophila. That the human homologs kept the same name is another issue. And if you think sonic is bad, consider sevenless, son of sevenless, junk (JNK)  and smack, mothers against decapentaplegia (mad), the list goes on. Drosophilists are kinda weird :P

@anongoodnurse: I think you may be mistaking the source of the name "luciferin".  It's from the Latin for "light bearing", and only (sort of) coincidental that it also happens to be a name for the devil figure from Christian mythology.

@terdon - Wow, I had no idea how... unusual some of those names could be.

@jamesqf - Please don't get me wrong; I love the name 'luciferin', and always have from the beginning. I admire wit (Wilde, Burns, Pope, etc.), and wish I had more of it. But it would surprise me if the researchers who named it were oblivious to the name of the mythological fallen angel.

@anongoodnurse: Not oblivious, no, but also not directly referencing it.  To name a luminescent protein "light bearer" seems obvious.  See also "luciferase", and remember that an old word for the common match was "lucifer".

Because their shape reminded researchers of rolls of Sushi (Ichinose et al, 1990):

These repeats were initially called GP-I structures because they were first identified in $\beta_2$-glycoprotein I. More recently, they have been called short consensus repeats or sushi structures because of their shape.

I thought it would be cool to add in a quote here from the paper, giving the explanation of the name in the authors' own words. Then I realized the paper you cited is merely a review that claims "More recently, they have been called…sushi". Following the next sentence is a citation to this paper, but that one never uses the word sushi. I'm curious if you know who the first author to use this term might be.

@CodyGray No idea. A lot of these terms enter the lexicon in labs and at conferences before they ever reach the literature.

Rumors of free alcohol offered in research conferences are completely untrue. I swear!

@terdon You're going to the wrong conferences, mate ;)

Special thanks for @JackAidley and also thanks for all the other comments.
I surmised that the explanation would refer to the shape of proteins, but I couldn't find any source which would tell me so. I also thought that it might be attached  to some kind of background story - my own example with precomplex Bötzinger - its name comes from Bötzinger wine served at the symposium in Heidelberg when discovery of this structure was first presented. You can never be 100% sure when it comes to weird names in science and their origins. Examples are numerous.
Once again, thank you very much!

@jack maybe. I don't really remember, it's all a bit of a haze. ;)


text:
How to distinguish processionary from other caterpillars
Processionary caterpillars have a vast and harmful presence in southern Europe. In northern Italy, in parks and gardens, I often see caterpillar nests in trees, but I do not know how to tell if they are processionary, with dangerous urticating hair, or other innocous (for humans and pets) kinds of caterpillar (such as tent caterpillar, for example).
I've read from Wikipedia and other sources that processionary "usually" nest in pines and oaks, but it is not clear to me if it is only a matter of preference or if they cannot nest in other trees. Does seeing a caterpillar nest in an another kind of tree safely imply that it is not a processionary nest?
Besides, the photos I have found show very different kinds of caterpillars,  what easy visual clues could I use to tell them apart? Ideally, I would like to be able from a distance to decide if I should get my dog away from an "infested" tree or if I can safely ignore it.

Hi, and welcome to Bio.SE. Your question could use a bit more context to demonstrate that you've tried answering this on your own. We always ask that the poster provide some evidence of prior research. Thanks!

I've tried to explain a bit more context in an edit. I know nothing of entomology, it is hard for me to find specific sources besides a generic internet search, which has not helped me so far, hence the question.


text:
How does alum help in blood coagulation?
I recently came across a test in my chemistry book which says that potash alum, $\ce{K_2SO_4.Al_2(SO_4)_3.24H_2O}$ is used on cuts and bruises, because it coagulates the blood quickly. The explanation it gave, was that blood is a colloid of proteins in water and the $\ce{K^+}$, $\ce{Al^{3+}}$ and the $\ce{SO_4^{2-}}$ ions coagulate(=precipitate) them, causing a blood clot (quickly). However, from biology, I know that blood coagulation(=clotting) is brought about by formation of fibrin network which traps the WBC and RBC in blood. The formation of fibrin from fibrinogen involves a series of reactions with many factors like $\ce{Ca^{2+}}$ , but not $\ce{K^+}$ or $\ce{Al^{3+}}$.
So, I was wondering what the actual explanation might be.

Do people actually use alum to stop bleeding, or only as a disinfectant? Does alum have any disinfectant effects?
Does precipitation of proteins in blood help clotting?
Does alum contribute in any way to the process of blood clotting?

Note: This is a question involving both chemistry and biology, but I posted the question here as I thought that this is more of biology than chemistry.

If English is not your native language, please use a spelling checker, especially for the titles of questions which are indexed. Every web browser has one built in — just set the language temporarily to English.

I will answer the three questions one at a time. Lets begin with the first one:

Do people actually use alum to stop bleeding, or only as a disinfectant? Does alum have any disinfectant effects?

Yes, alum is also used as a disinfectant, and it works in the same way as it does in blood coagulation. In aqueous solution, potash alum dissociates as:
$\ce{K_2SO_4.Al_2(SO_4)_3.24H_2O -> 2~K^+ + 2~Al^{3+} + 4~SO_4^{2-} + 24~H_2O}$
Now, as is known, blood is a colloidal solution, in which the plasma proteins are charged (see Rügheimer et al, 2008). These ions from alum neutralize the charges on plasma proteins, causing the blood to coagulate. Similar effect is observed in disinfectant where these ions react with the free organic acid and thiol groups of proteins on microbes and free proteins, resulting in their precipitation (Williams, 2001). Thus alum can act as disinfectant.

Does precipitation of proteins in blood help clotting?

Coagulation of both plasma proteins and RBCs takes place on application of alum, since both of them are charged (Fernandes et al, 2011) as is discussed in next point. However, it is difficult to say whether coagulation of plasma proteins plays a significant role in clot formation or not.

Does alum contribute in any way to the process of blood clotting?

Yes, alum does contribute in the process of clotting: it makes clotting faster. Although the term 'clotting' is generally used for formation of what is called as platelet plug, the actual process of clotting also depends on coagulation of colloidal particles in blood. When the blood is exposed to the extracellular matrix (due to damage to blood vessel), platelets activate and, via a cascade of reactions, lead to formation of a platelet plug. Red Blood Cells get tapped in this plug (which is actually a fibrin meshwork) and lead to formation of clot. A nice and simple representation of this process is below (from here):

Without alum, RBCs would take longer to coagulate due to mutual repulsion. By neutralizing them, alum makes this process easier and faster. Hence, alum helps in the formation of blood clot via coagulation of red blood cells.
I hope this helps.


text:
Single copy housekeeping genes
I am working on a tool for SNP calling in polyploid plants. To test my method, I need a list of housekeeping genes common in almost all plants. For my case, these genes must be single copy (ie each HK gene should have no paralogs).
Briefly I need a list of genes that are:

House keeping
Single copy
Common in almost all genomes, or genomes of a taxa

Any help is appreciated.

If you talk about animals, globin might fit in all criteria...

I found this to be relevant https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203353/

Just flying from the waist: filter approach:
If there is a data source that has the expression data for cells in multiple tissues for any organism i would use that to find the housekeeping genes by sorting which genes are expressed in the greatest number of cells (think excel or XML). Next, I would check which of those genes are also found in/similar to the respective gene (homolog I thin its called) in the plants (using genome browser, e.g., ensembl and blast or just look it and click on the button to bring you to the plant genome). If your model organism does not have sequenced genome... get primers and see if you can sequence it for yourself to see if its there. Then check to see if its a single copy. Hardest part is finding an expressome database spanning multiple tissues in an organism to find housekeeping genes - then hoping they are conserved to the plant. Alternatively, you can consult literature to find housekeeping genes.
You probly just wanted a listing of the genes... sorry.

There is no single answer for a gene. The most correct thing to do is to use a set of genes across many locus and measure the correlation of copy number across them first, and only use the ones which co-segregate as single copy number as the measure of 'one copy'.
This is the same approach used for qPCR and is the basis of the widely used geNorm algorithm (11k citations). While in qRT-PCR the 'stability' of a gene expression is compared across mRNA which are at different stoichiometry, in your case you just further restrict that the genes should have stable stoichiometry.
If I was designing this, I would use the same set of genes which are 'housekeepers' defined in the two publications above and avoid sex chromosomes.

The following is probably a good set, it's for Arabidopsis you need to check if it fits with your need.
CBP20 Gene
Gene Locus: At5g44200
Actin-2 Gene
Gene Locus: At3g18780
UBC Gene
Gene Locus: At5g25760
SIGMA sells primers set for these: http://www.sigmaaldrich.com/life-science/molecular-biology/plant-biotechnology/plant-molecular-biology/control-primers-for-arabidopsis.html


text:
First infection of malaria
As I know Plasmodium falciperum survive in either a host animal, human or mosquitoes.
But how does malaria come to infect either of them initially?
I am interested in knowing evolution of malaria. How it infected first mosquitoes when neither human nor any other mosquito was infected?

Could you provide some clarification of your question? Are you wondering how malaria evolved a multi-host life cycle? Or are you more concerned with how malaria is transmitted between a new host-vector cycle?

@hamilthj i know malaria resides either in mosquitoes or infected bitten animal, question is how it infected first mosquitoes , where did it come from

Great, I'd suggest clarifying that in your question to highlight your interest in the evolutionary origin of malaria


text:
Why does Edema occur in Kwashiorkor?
Edema in lower leg and face is a symptom of Kwashiorkor. It is the most distinguishing feature of it which distinguishes it from Marasmus. Why would decrease in amount of proteins cause Edema? Why doesn't it occur in Marasmus (which is both protein and energy deficiency)?

I thought I might add that there are many factors that can lead to edema, and the primary cause of edema in different individuals with the same condition may not be the same. On malnutrition such as in Kwashiorkor, many of the bodily systems are compromised. As mpribis said below, abnormal cardiac activity can contribute, as can kidney and liver failure. I suffered from severe edema of the legs due to malnutrition and different doctors attributed different things to the edema; namely, blood tests showed electrolyte imbalance, raised serum albumin and deranged liver enzymes

Why would decrease in amount of proteins cause Edema?

Proteins in the blood (esp. albumin, because it's the most abundant one there) cause fluid to come from the interstitial space into the capillary. This phenomenon is called oncotic pressure. On the other side there is hydrostatic pressure on the vessel wall, which causes fluid to exit the capillaries. This hydrostatic pressure gets lower as the blood passes through the capillary, while the oncotic pressure stays the same, because under normal conditions, proteins don't exit the capillary very much compared to their amount in blood.
In the first part (closer to the arteriole), hydrostatic pressure is bigger, so the fluid exits the capillary site, while as you get closer to the venous site, the hydrostatic pressure gets lower than the oncotic pressure and the fluid flow is reversed. (see picture)
If you lower the amount of proteins in the blood drastically (as in Kwashiorkor) the oncotic pressure is lower and therefore less fluid is reabsorbed from the tissue, which leads to its accumulation there - this results in edema.

Why doesn't it occur in Marasmus (which is both protein and energy deficiency)?

Sometimes, both features of kwashiorkor and marasmus are present in the patient, which is called marasmic kwashiorkor and the distinction between these two conditions isn't that easy.
However, normally in marasmus, there is also dehydratation present, which balances the effects of decreased oncotic pressure. Cardiac output is usually decreased too, which leads to decrease of hydrostatic pressure, so again, this can counterbalances the decrease of oncotic pressure.

Oedema in malnutrition(kwashiorkor) is due to extra cellular imbalnce of the fluids which is caused by lower albumin level. Where some can see protruded stomach due to enlargement of liver this is caused by imbalance in gastro intestinal system hence causing gut and liver to swell hence diognosed as oedema.


text:
unsaturated fatty acids and hydrogenation
what is the need to hydrogenate unsaturated fats?
When we hydrogenate the unsaturated fatty acid, we eliminate double bonds by adding hydrogen atoms, and this straightens out the natural bent shape of the unsaturated fatty acids. But why would we choose to hydrogenate unsaturated fatty acids before consuming them?

It makes them (more) solid.


text:
Algae or Lichen identification. Coastal BC, Canada
I have tried all books and internet resources I know of, but I still have no idea what this might be — a lichen or something else.
At first glimpse, I thought it was something man-made and unnatural, but then I looked closer and saw how it appears to be attached and growing. It grows on exposed rocks well above the high tide. The photo is taken in late March, on northern Vancouver Island. It's loosely attached to the rock.
It was somewhat abundant around the general area (within of a few km), but I haven't seen it elsewhere - although I'm not from BC so there might be a lot of this around.

The water droplet in the lower right corner give a rough sense of scale.
Edit:
Adding another photo in which I just noticed a streak of white, which I included in original resolution.

Possibly small (young) specimens of Usnea rubicunda

The growth pattern doesn't appear to match any photos or description of U. rubicunda I've seen, but it's not like I've got a better suggestion. Added a 100xp bounty to whoever gives a plausible answer. Maybe it's not even a lichen (But what else?). I regret not having taken a sample of it home, thought it'd be easy to identify given the color...

I want to propose you expand your search to a broader taxonomic scope. Specifically, I think you might be looking at a species of "red" green algae (family: Trentepohliaceae).

From Nelson et al. (2011):

All Trentepohliaceae have filamentous growth forms and often contain large amounts of carotenoid pigments (ß-carotene and hematochrome), causing the algae to appear yellow orange in color (Thompson and Wujek 1997, Lo´pez-Bautista et al. 2002).

The Trentepohliaceae contains five genera: (Trentepohlia, Printzina, Phycopeltis, Cephaleuros and Stomatochroon) and 70+ species worldwide.

For example, the following algae (picture from England) looks fairly similar to your specimen:
Trentepohlia aurea

 Source: David Fenwick
If your specimen is a species in this family of algae, it is most likely in the Trentepohlia genus (or possibly Printzina genus).
Trentepohlia is a genus of filamentous chlorophyte green algae in the family Trentepohliaceae.

Typically orange or yellow in color.
Live on tree trunks and wet rocks or symbiotically in lichens.

Here's a picture of a free-living Trentepohlia species from coastal Oregon, USA:

 Source: Richard C. Hoyer (2015)

The source notes that the specimen was simply ID'd as "Trentepohlia sp." by Tim Rodenkirk (Botanist with the Coos Bay BLM in North Bend, Oregon).

That seems like the right genus and I lift my hat in honor to you. Thank you for an excellent answer! I did doubt that it was a lichen, but I just couldn't think of what else it might have been as I was unaware of terrestrial algae with such a growth.

Excellent find! I am surprised to see filamentous algae growing in such a dry habitat. Usually they grow under water or in very wet conditions.


text:
Do ants see, have brain?
I'm new here and I would like to know if ants can see, I mean with their eyes not with antennas: I was walking around and found an ant specy,  they were reacting when I moved my fingers towards them, as if they were seeing.
I would also to know  do they have a "brain" and what I'm the most fascinated by is how do they find their way?
PS: English is not my local language that's why my vocabulary is limited. Please feel free to correct any mistakes and or improve my words. Thanks

Related question : 1) https://biology.stackexchange.com/questions/19848/how-do-ants-know-where-they-are-going-without-eyes 2)https://biology.stackexchange.com/questions/56654/how-do-ants-follow-each-other

This question was flagged as off-topic and it doesn't really answer my question. But thanks pointing out.

I just told related questions, that if you are interested you can have a look at it :)

Yes, thank you. I found some useful informations there.

Welcome to Biology.SE! What research have you done before asking it here?

Ants do have eyes, though how well (and even whether) they see depends on the ant. They also have brains.
You aren't wrong to put quotes around "brain" since in many organisms the nervous system isn't as centralized as in vertebrates, and when they do have concentrations of neurons in various places ("ganglia") it isn't always in the head, and the one in the head isn't always significantly larger than the other ones, so it's often hard to call that having a brain. This can be true of many insects:
http://cronodon.com/BioTech/insect_nervous_systems.html
Having said that ants do have a centralized nervous system, with the neurons in the head making a larger percentage of their body than most other insects, i.e. they have brains. It appears social insects tend to have larger brains for their body size, which includes bees and ants.
http://guides.library.harvard.edu/fas/Brains/ants
Ants also have eyes; they're just often too small to see clearly, especially when the ant itself is small and the eyes are the same color as the ant's head. Ants descended from wasp-like ancestors that probably had quite good eyes, like modern wasps and bees do. But ants mostly live on and underground and don't need eyes as much as flying, pollinating insects do, and how well ants can see varies a lot between the species.
Or I'll just quote Wikipedia:

Like most insects, ants have compound eyes made from numerous tiny lenses attached together. Ant eyes are good for acute movement detection, but do not offer a high resolution image. They also have three small ocelli (simple eyes) on the top of the head that detect light levels and polarization. Compared to vertebrates, most ants have poor-to-mediocre eyesight and a few subterranean species are completely blind. However, some ants, such as Australia's bulldog ant, have excellent vision and are capable of discriminating the distance and size of objects moving nearly a metre away.

And the cite for that latter example:
ATTACK  BEHAVIOUR  AND  DISTANCE  PERCEPTION
IN THE  AUSTRALIAN  BULLDOG  ANT
  MYRMECIA
NIGRICEPS
Those same ants even have color vision it seems. Conversely, African army ants appear to be blind, although even that depends on the caste. From Sociobiology of the hypogaeic army ant Dorylus:

On workers:

Eyes are either reduced or absent.

On males:

Army ant males do indeed resemble wasps, having large and robust bodies and well developed eyes and wings

So it's very possible the ants you ran into could see your fingers.

This is good answer. I am curious that ants use pheromones to know who is who or who is the queen?


text:
Why human endometrium doesn't stay constant?
Is there any explanation or evolutionary advantage to the endometrium constantly cycling between the proliferative and menstrual cycle? Wouldn't it be more advantageous if it kept always fully thickened? I imagine it is less energetically expensive than to be always producing and losing all those cells, blood vessels, etc.

One hypothesis is to protect the uterus and oviducts from sperm-borne pathogens.
Also Beverly Strassmann has proposed that the energy savings of not having to continuously maintain the uterine lining more than offsets energy cost of having to rebuild the lining in the next fertility cycle, even in species such as humans where much of the lining is lost through bleeding (overt menstruation) rather than reabsorbed (covert menstruation).


text:
After fat is burned from one part of the body, is fat moved around the body?
If you go running, for example, and burn fat from your legs, does your body send fat from other parts of the body to that area? If so, why would it do this?

Fat burning is a generalized procedure so there is no such a thing that some part of body loses fat and other part gains it.
Targeted Fat Loss still is a myth.


text:
Are there ways to genetically increase mutation rate of E.coli?
Are there ways to increase mutation rate of E.coli using genetic modifications? I know possible ways it can be done without genetic modifications by exposing the cells to stressful conditions like anaerobic and radiation but what are some genetic ways?
Thanks!

Mutations are caused by the insertion of the wrong bases during replication, or by chemical changes to bases, either by chemical agents or by radiation.
The rate of mutations could be increased by exchanging the E.coli polymerases with other polymerases displaying higher error rates (or with less proofreading capabilities). A lot of errors are quickly repaired via different mechanisms, knocking out all or a few of those mechanisms might result in an E.coli strain with an increased mutation rate (if they survive).
https://www.ncbi.nlm.nih.gov/books/NBK9900/
A more elaborate way would be to engineer E.coli to contain a pathway that synthesizes a mutagenic compound. The easiest way to to this would be 1 enzyme that generates reactive oxygen species, as those also cause DNA damage. You could also delete some of the catalases and other enzymes that remove reactive oxygen species instead.
https://www.ncbi.nlm.nih.gov/pubmed/16824196


text:
What am I looking at in Franklin's Photo 51 of DNA?
Here's Rosalind Franklin's famous Photo 51, the X-ray diffraction image of DNA from which Watson and Crick deduced its structure:

My understanding is that it depicts a short segment of DNA shown from the side (so the axis that the strands wind around would run up and down through the center of the photo). Like this double-helix diagram from Watson and Crick's paper:

I have a lot of trouble connecting the photo to the diagram.
What am I actually seeing in the photo? There are dark blobs at the top and bottom. A diamond shape of dark lines. A concentric circle (or rounded diamond) inside the outer diamond. An X formed from two intersecting rows of 7ish mostly horizontal short lines or blobs. Which of these features correspond to what parts of the DNA molecule?

@another'Homosapien' Just Wikipedia and Google. There's a smorgasbord of info about the structure of DNA and about the history of the photo, but I was unable to find anything directly labeling the structures shown in the photo and relating them to the diagram. Forgive me if I missed something obvious.

The interpretation of this image is not as easy as you think, but it took me less than a minute to find this.

@another'Homosapien' That link is interesting, but it does not explain what OP wants. I believe he wants this: https://www.quora.com/How-does-one-physically-interpret-the-different-diffraction-patterns-between-A-DNA-and-B-DNA. And here the detailed paper: https://www.unamur.be/sciences/physique/udp/documents/Francis-Crick-JCE-paper.pdf

@another'Homosapien' I also found that and read it, but unfortunately I don't understand it. It says that the large dark patches at top and bottom "represent DNA’s ‘bases’", but then goes refers to the smaller "ten blobs" as "ten bases", so it left me a bit confused. I was hoping for something more definite and specific.

I just gave an example link. It was just to tell that its not very difficult to find such papers, seeing that @GerardoFurtado has found a couple more links ;)

@GerardoFurtado Yes thank you that is exactly what I was looking for!

@GerardoFurtado Do you want to make this into a real answer? Would be great...

@Chris Well, to be honest, it seems like cheating to me, since I already linked the paper! But the link is here, if anyone wants to make a good explanation based on it, please feel free to do it.

@GerardoFurtado Why? You digged out the relevant paper, so I think you deserve the credit for this.

@Chris OK, I'll give it a try.

Your opening statement is incorrect - "Here's Rosalind Franklin's famous Photo 51, the X-ray diffraction image of DNA from which Watson and Crick deduced its structure" - Watson and Crick did not deduce the structure from the picture alone. They were able to do so because they already had a host of information about the structure and had been working on the problem for some time. If it were a matter of simply looking at the picture, Franklin - who was far more skilled at this kind of crystallography - would doubtless have rapidly identified the structure.

Like Gerardo, I thought this was down the long axis - I also did some re-reading into the issue thanks to this question and discovered the photo was actually Ray Gosling's, not Rosalind Franklin's. I can't even confirm whether she was (formally) his supervisor; it sounds from another source (with better references than Wikipedia) that she wasn't officially eligible to supervise students because of the position she held at the time. I'll probably put together a proper question about this later when I have time.

Separate question now posted: https://biology.stackexchange.com/questions/59015/was-raymond-gosling-supervised-by-rosalind-franklin

Well, you said that you...

...have a lot of trouble connecting the photo to the diagram.

And that's quite excusable: interpreting that X-ray image is actually very complicated .
All the quotes and images in this answer, except the bulleted list further down, come from this paper (Lucas, 2008), which explains that historic picture in details.
Full disclosure: I always though that that image depicted the X-ray going longitudinally (that is, along the main axis) through the DNA. However, it goes transversely:

When filamentous macromolecules are packed in a fibre along a fixed direction, the X-ray intensities diffracted by the fibre fall on the observation screen along approximately straight and equidistant lines, the so-called layer lines, perpendicular to that direction. This important concept was introduced by Michael Polanyi in 1921 for the X-ray study of cellulose. (emphasis mine)

These are the so called layer lines (I'm keeping the original paper's legend in all images):

Then, still according to the paper, Crick and others started to hypothesise how would be the X-ray diffraction in a monoatomic helix:

In 1952, Cochran, Crick and Vand developed an analytical theory for X-ray diffraction by a monoatomic helix. The immediate interest of their theory was to give a transparent, analytical expression of these amplitudes at a time, in 1952, when computers, if at all available, were barely capable of a brute force calculation of the total diffraction intensity.

This is the X-ray diffraction pattern in a monoatomic helix, which is quite important to understand the famous DNA diffraction image later on:

Thus, with that theoretical background, we can understand our famous image:

In this image, a X-ray diffraction image of A-DNA (left) and the more common B-DNA (right) show a periodic pattern in the layer lines.
The diffraction patterns can be interpreted as follows (source):

The layer line separation reveals the value of the polymer repeat period. The decrease of over 20% of the layer line spacing when going from A to B implies an increase of that much in the period: P = 2.8 nm for A-DNA and 3.4 nm for B-DNA.
Look at the sharp, discrete spots observed near the center of the
diffraction pattern for A-DNA along the first few layer lines, these
suggest the crystalline order in the fibre. In the high-humidity
B-DNA pattern, these crystalline spots are absent, suggesting that
the extra water molecules must have invaded the space between the DNA
molecules, freeing them from being locked into crystallites.
The thick arcs at the top and bottom of the B-DNA pattern are found at approximately 10 layer line intervals from the center, implying that B-DNA had 10 repeating units within one period of 3.4 nm. These are produced by the scattering of X-rays by the equidistant, nearly horizontal flat bases separated by 0.34 nm. The A-DNA pattern lacks these big smears, suggesting that the bases in A-DNA are not horizontal, and the number of base pairs per helical period is closer to 11.
The central cross in B-DNA represents the Saint Andrew cross expected
from a helical molecule. The large radius r (1 nm, indicated by the
meridian angle of the cross) and the absence of intensity in the
meridian diamonds indicates that the phosphate backbone is at the
periphery of the helix. This cross appears to be absent in A-DNA,
however, this is due to destructive interference from some of the
inclined base pairs.

Finally, this is an image better relating the double strand structure of the DNA (both A and B DNAs) with the X-ray diffraction image:

Reference:
Lucas, A. (2008). A-DNA and B-DNA: Comparing Their Historical X-ray Fiber Diffraction Images. Journal of Chemical Education, 85(5), p.737.

IIRC, in The Double Helix (a controversial source to be sure), Watson claimed that the major impact of the image was that it allowed a particular angle to be measured, which allowed them to turn their idea of a double helix into an actual atomic structure (since the angle was only made possible by the bond angles of that particular molecular arrangement). Rosalind Franklin’s image was published in the same journal as Crick and Watson, though at the time she (and the editors) believed it was an independent corroboration of their structure, rather than a crucial piece in determining it.

Terrific answer. Thank you for such a thorough and understandable explanation.


text:
Septic Shock: I'll kill myself before you kill me
Most of the deaths caused by extracellular bacteria don't actually result directly form their action. Rather, it results from an overreaction of the immune system to antigens such as LPS and LTA (Superantigens are bacterial toxins with an enormous power in originating immune responses; they are able to activate numerous T cells through a different TCR, which will produce too many pro-inflammatory cytokines, resulting in an excessive reaction by the body and causing self-tissue damage, etc), and it is this excessive reaction of the immune system which ends up killing the organism.
http://www.medicalnewstoday.com/articles/311549.php
http://www.medicalnewstoday.com/articles/305782.php?sr
How come, after all this evolutionary time, we have this self-killing mechanism? Why do T-cells have receptors to such generalized and potent antigens, which will frequently result in self-damage? Is it because at the point of infection that this happens, we would die anyway from it, so it doesn't alter fitness?

Sounds very interesting. Can you please support your claim that Most of the deaths caused by extracellular bacteria [..] results from an overreaction of the immune system to antigens with a reference?

@Remi.b sure, I think it is all very clear here: http://www.medicalnewstoday.com/articles/311549.php
also here: http://www.medicalnewstoday.com/articles/305782.php?sr

@Remi.b this is also interesting: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422540/

the mechanism exists to protect against the spread of infections, the infection cannot utilize the cells to make more copies of themselves if the cells suicide when infected, this is a perfectly normal response to low level infections, sore throats for instance are often caused by this response. Additionally animals that reach the point of septic shock (massive widespread infections) would rarely survive anyway. so the question you should ask is without any form of medical intervention is the individual actually less likely to survive without this response.

@John the question is somewhat that, is there a chance that organisms who died from septic shock would have survived if the immune reaction was less strong? because if yes then it would make sense that we had evolved in that direction.

@John in this case I was talking specifically of extracellular bacteria, which don't grow and reproduce inside host cells, so the death of host cells to prevent that wouln't fit here

Ignore most of my statment, I was thinking of a different antigen response then you are talking about. Although I should mention none of your sources indicate percentages of extra to intracellular infection in sepsis. As for septic shock survival the question is whether MORE would survive, because weakening the immune response is going to get some killed. Almost everything in biology is a cost benefit trade off. this paper has a good description of the benefit of various immune responses during sepsis. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422540/

This excerpt is also relevent.  http://www.birmingham.ac.uk/Documents/college-mds/facilities/cis/Essentialimmunology/Chapter1.pdf  "Mice deficient in tumour
necrosis factor are protected fromshock induced by lipopolysaccharide but on the other hand are
more likely to die from overwhelming bacterial sepsis. This illustrates the fine line that the immune
system has to tread between evoking protective immunity and killing the host."

@John yes, but knocking out TNF is an extreme deficiency in the immune system. I was thinking more of something like the organism being able to detect when the immune response is causing too much, potentially fatal host damaged, and then downregulating it a bit

@John yes, the question should then be if having that mechanism would pay off, meaning less individuals would die from weakened immune response than from an excessive one.

which is an entire new system (which could also be exploited) for an exceedingly rare circumstance. Remember the rarer the event the less evolution will be able to prepare for it becasue it is overpowered by more common selective pressures.

@John true, although I doubt apart from modern times that it was of such rarity

Which shows how well the current setup works, consider people prior to the invention antibiotics and germ theory, people routinely lost limbs and survived so the existing system obviously works for preventing sepsis. The only time septic shock comes into play is under circumstances people were unlikely to survive in the first place, severe sepsis. You can see how fast response is more important than a measured response. Preventing severe sepsis would be more important than mitigating it under natural conditions.

@John but not to the point of killing itself. I imagine there must have been a lot of deaths from septic shock caused by, say, a severe urinary infection, whereas if the response were more contained maybe they would have survived

Let us continue this discussion in chat.

The important thing to recognize about the host response to sepsis is that it is actually a generalization of mechanisms used in local infection response by the innate immune system. When an animal has a local infection, such as at a wound site, innate immune cells such as monocytes and macrophages recognize 'generic' bacterial features, such as lipopolysaccharide (LPS). When they recognize these features, they respond by engulfing the pathogen and releasing cytokines that result in local vasodilation and inflammation. In this context, these responses are close to ideal. Vasodilation helps to isolate the area and promotes the recruitment of more immune cells.
These sorts of small infections are very common for all animals (just about every creature cuts itself at least once), including humans, and the absence of this response would result in sepsis (not the immune response, but just sepsis itself) because the infection would not be contained. Control of such local infections is thus 'life-or-death' for all creatures—which is an extremely powerful selective pressure.
The other thing to consider here is when in nature are these local defences overwhelmed such that sepsis, and then septic shock, which is what you are asking about, occurs. The answer is that it does not happen very often. Transient bacteremia is relatively common (it even happens when you brush your teeth, see this paper for example), but overwhelming bacteremia, sepsis, is not very common in healthy individuals. It is generally a condition that affects weakened individuals and those who have already reproduced. We notice it far more now because it is a major cause of death for humans hospitalized for other conditions, as well as older people with pneumonia. Most of the primary causes of sepsis though—major wounds, pneumonia, weakened immune systems—would be death sentences in themselves in the absence of medicine, irrespective of the organism's response to the sepsis.
That is not to say it is completely invisible to selection, for example this paper, and others like it, demonstrate that the immune cells responsible for septic shock are regulated by hypoxia (a major feature of shock). However, it is reasonable to say that any fitness advantage conveyed by a reduction in the intensity of septic shock would be dwarfed by the fitness penalty paid if that reduction also reduced the efficiency of the response to local infections. For this reason, it is likely that septic shock is an evolutionary accident, a trait that exists in part because it is irrevocably linked to a set of highly advantageous traits (those involved in local infection response), rather than a trait that has been extensively selected on by evolution.
Note that this answer is my opinion only. To the best of my knowledge, there is no definitive answer to this question yet, and future research may prove me wrong.

Welcome to Biology.SE! Seems like you are quite familier with how ideal answers are posted here ;) +1 for the effort, and this comment, just to appreciate the nice content in your first answer! :D

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Do ectotherms think slower when they are cold?
Animals near the ectotherm side of the endotherm-ectotherm spectrum rely on external heat sources to regulate their body temperature. When they are cold, overal enzyme activity and metabolic rate is lower.
My question is if these animal tend to 'think' slower when cold?
To be honest, my knowledge of brain physiology is very sketchy, I'm not sure biochemical activity plays a large role vs. electrical and diffusion processes and the latter would be less temperature dependant. So I'm not sure we would expect ectotherms to 'think' slower.
OTOH, wikipedia on endotherms states ...

Some ectotherms, including several species of fish and reptiles, have been shown to make use of regional endothermy, where muscle activity causes certain parts of the body to remain at higher temperatures than the rest of the body. This allows for better locomotion and use of the senses in cold environments.

The source for this claim is on google books, just not the relevant pages (Willmer, Pat; Stone, Graham; Johnston, Ian (2009). Environmental Physiology of Animals)
I'm also not sure how to define 'thinking' within this wide range of animals, I'll take any metric for  speed at cognitive tasks or reacting to external stimuli.

if the lower temperature would make the transmembrane proteins responsible for the maintenance and restore of resting potential, and creation of action potential, work slower or less, I believe it would make the thinking slower. On the other hand, the lower temperature may only alter the strength of the stimulus necessary for the action potential, in which case I don't know if the thinking would be slower or if the only change would be that there would simply be less thinking. I believe both happen, but to be sure one needs to analyze this to a deeper physiologic level and do some calculations

temperature definitely affects insect response time, not sure about other ectotherms. https://www.biorxiv.org/content/biorxiv/early/2016/06/09/056051.full.pdf

I would assume as the temperature decreases, even as an ectotherm organism that the neuro processes would decrease. From my experience in chemistry, the colder the temperature the slower the molecules vibrate. As a result, it would take a longer time for the sodium and calcium molecules to move from the end of the neurons to the synapses resulting in delayed thinking. If they are absorbing the energy necessary, then their neuro processes should be functioning normally.

Welcome to Biology SE and thank you for your contribution! However, we tend to prefer answers that are backed-up by references in this community. As it stands this is really a comment, not an answer. Additionally you seem to be contradicting yourself: will the "molecules" diffuse slower or will the "processes" be functioning properly?

It's usually not simply that it would take longer for the ions to move during depolarization. It's much more complicated than that, usually involving a myriad of interactions. A large part of it is that metabolic processes slow down (remember, activation energy often requires heat), and less energy in neurons means they will respond sluggishly.

I can't see why it would be different for ectothermal animals than endothermal animals. By lower temperatures, I'm not considering a few degrees one way or the other; there is probably a maximal temperature range for the nervous system to operate, followed by decreases in lower ranges.
You write

Some ectotherms, including several species of fish and reptiles, have been shown to make use of regional endothermy, where muscle activity causes certain parts of the body to remain at higher temperatures than the rest of the body. This allows for better locomotion and use of the senses in cold environments.

Protective mechanisms are also in place in humans, where shivering generates heat, and blood is shunted away from cold areas to core (warmer) areas to protect executive functioning (thinking) and heartbeat regularity. It doesn't mean that once thes compensatory mechanism (and others) are overcome by falling temperatures, that cognition remains unaffected.
Given extremes, there are iguanas falling frozen (not necessarily dead, though) from the trees in Florida. I doubt they even know they're falling. Maybe a muddled "Huh?" when they hit the ground, a car, etc. But I would wager that, could we read their thoughts, they are not racing with anxiety:

My ---, I'm stiff as a board! Someone help me, I can't move a muscle! What's happening? Is this a bad dream where I can't move? Am I dead? Is this HELL? Oh, ---, I wish I had spent more time with my wives and kids! Is a deathbed confession acceptable now? Can anyone hear me? Am I even talking? How could I be talking if I can't move my mouth?!

Hypothermia definitely slows down thinking in humans, e.g. in studies to try to understand the effect of cold on astronauts (not done on astronauts, though):

Chronic multifactorial stress impaired cognitive function and mood; the addition of moderate, acute cold stress further degraded vigilance and mood. When such circumstances occur, such as during disasters or military operations, measures to prevent adverse cognitive and physiological outcomes are recommended.

and

Cold stress is experienced in occupational (military, fishing trawlers, emergency disaster workers) and athletic (winter sports) settings (Muller et al., 2012). It appears that both moderate and extreme reductions in ambient temperature may have a negative effect on cognitive function (Banderet et al., 1986; Palinkas, 2001). Specifically, cold exposure (−20 to 10°C) has led to decrements in memory [complex task (Thomas et al., 1989; Patil et al., 1995)], vigilance [complex task (Flouris et al., 2007)], reaction time [simple task (Teichner, 1958; Ellis, 1982)], and decision making [complex task; see Table Table4;4; (Watkins et al., 2014)]. Such consistent findings across such diverse ambient temperatures may be explained by traditional theories of cold induced cognitive decrement (Teichner, 1958; Enander, 1987; Muller et al., 2012). ... Regression analysis from a recent study (Watkins et al., 2014) reported a significant relationship between alterations in thermal comfort and cognitive function in the cold.

So, yes, at sufficiently lower temperatures, cognition is decreased. One theory is that initially it is decreased because attention is directed at the discomfort of being cold (1958), but fMRI studies might clear up that issue nicely.
Cognitive function and mood during acute cold stress after extended military training and recovery.
The Impact of Different Environmental Conditions on Cognitive Function: A Focused Review


text:
Is it possible to produce a tangible mass of DNA/RNA using a PCR reaction?
A Polymerase Chain Reaction (PCR) is a method of amplification which enables one to produce many copies of a certain DNA/RNA strand for many applications (as described in the link above).
I have never seen the actual process and the resulting PCR solution, but according to Wikipedia, the volume of the solution is of the micro- to milliliter magnitude.
I was wondering: if this process were allowed to continue on and on, while supplying all necessary nucleotides and other materials, to the magnitude of, say, liters - could we end up with a tangible mass of DNA/RNA? In other words, will we be able to extract from the solution a solid mass of DNA/RNA that is visible to the naked eye? If yes, can we predict the physical characteristics of such mass?

PCR amplifies only DNA not RNA.
A PCR reaction is typically within the  micro liter volume, and can go down to the nano liter volume for qPCR. The maximum volume of a PCR tube is 200 microliters. The maximum volume a 96 well thermocycler can handle per well is usually 100 microliters. So the maximum amount of reagent volume one thermocycler can handle at a time us 9.6ml
I have never seen anybody scale a PCR to mili liter volume, as that would be rather expensive and excessive.
However if some some reason, somebody did do as you say, yes it is possible to obtain visible quantities of DNA. (Removal of impurities would be required first... ie unreacted dNTP, primers) And given that we can obtain visible quantities of DNA by extracting DNA from bacteria or salmon sperm.. I am sure a chemist somewhere would be able predict the physical properties of that DNA mass.

PCR on a milliliter scale can be useful e.g. for use as a template for large-scale in vitro RNA transcription. It's not the most common use for PCR, though.

Presumably, if we were to go through N PCR cycles and start with a few dozen litres of solution, I don't see any reason why there's be a limit to the amount of DNA PCR can produce. The limitation is only in the size of the machines available in the market, not in the underlying chemistry.

aside from machine limits, other limits are also present.. pyrophosphophate (PP) that produced went dNTP are polymerised is an inhibitor to polymerase enzyme.. Repeated heating will cause deamination of cytosine to form uracil.


text:
the meaning of "Non-primary hits" and "tags"
Can I ask you to help understand the meaning of "Non-primary hits" and "tags" in the following paragraph related to RSeQC:
The result table reports total number of reads (excluding nonprimary
hits) and tags (separate splice fragments of a read). Total assigned tags
indicate how many tags can be assigned unambiguously to the ten different
categories listed below.
Total Reads 49743155
Total Tags 63012643
Total Assigned Tags 57529077
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Group Total_bases Tag_count Tags/Kb
CDS_Exons 36821030 34763281 944.11
5'UTR_Exons 34901580 2856644 81.85
3'UTR_Exons 54908278 9772738 177.98
Introns 1450606807 8468986 5.84
TSS_up_1kb 31234456 94103 3.01
TSS_up_5kb 139129272 161914 1.16
TSS_up_10kb 249300845 217980 0.87
TES_down_1kb 32868738 789703 24.03
TES_down_5kb 142432117 1368378 9.61
TES_down_10kb 251276738 1449448 5.77
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =

"tag" is a weird term in this context. It used to mean "read", but RSeQC likes using it in an odd way. Suppose you have a read that aligns to a single contiguous (though possibly with InDels) stretch of DNA. This would then count as one tag. Suppose instead that you have a spliced read, that is one where part aligns to one exon and part to another exon. Each aligned part of this read then counts separately as a tag. So this 1 read becomes 2 tags. By extension, if you have a read that is spliced such that is starts in exon 1, jumps to exon 2, and then finally jumps to exon 3, then it'd count as 3 tags. This is only useful if you're interested in splicing, since the higher this value is the better you're able to discern differences there.
For "non-primary hits", suppose you have a read that can align equally well to multiple places in the genome. If there are 5 equally good alignments, then 4 of these will be labeled as "secondary" and one of them will not, which is then the "primary alignment". "non-primary hits" is then an odd way of saying "secondary alignments". The number of primary alignments is equal to the number of reads that aligned.


text:
Predict if a given protein can pass through the intestine
Assume that i have a 3d-protein structure in a PDB file on a computer.
Is there any bioinformatic method to predict if that protein can pass through the intestine or not?

No, you can only make such prediction with experimental data, such as pH stability and vulnerability studies with the relevant proteases.

You could start with a structural BLAST search, so a BLAST search against the Protein databank and look through the significant matches and search whether these can pass through the intestine (based on literate e.g.) and then align the PDB file of this BLAST match with yours. This will at least give you some information and as suggested by Jeppe further information could probably only be found using experiments.

@RickBeeloo that's a very smart idea.Thank you very much!


text:
Help with preparing Congo Red TSA
So I want to make Congo Red TSA. My instructor gave some hints but I still have some questions:

I start by making two stock solutions: 20 mg/ml of congo red and coomassie in two different falcon tubes. To prepare 30 ml of each, would I dissolve 600 mg in sterile water?
The final concentation in a 500 ml TSA solution needs to be 40 μl/mL of CR and 20 μg/mL of coomassie. How do I calculate the amount of solution needed for the TSA?

1) Yes, that's correct.
2) This is just a simple matter of applying the equation $C_1V_1=C_2V_2$. For congo red:

$C_1=20\frac{mg}{mL}$
$C_2=0.04\frac{mg}{mL}$
$V_2=500\ mL$

I'm sure you and a calculator can figure the rest out.


text:
Predict if a given protein is recognized by antibodies
Assume that i have a 3d-protein structure in a PDB file on a computer. Is there any bioinformatic method to predict if that protein is recognized by all known antibodies of human and cause an immune response or not?
If the answer is yes, how accurate of these method?

First of all: It is important to appreciate tha antibodies do not recognize antigens, they recognize epitopes borne on antigens.
There are several software (online) that allow to predict these epitopes with high accuracy. I´m going to describe some of them next:
Prediction of B-cell epitopes:
You have to be in mind that B-cell epitopes can be continuous and conformationals.
Continuous epitopes can be predicted using Bcepred. This prediction methods is based on physico-chemical properties on a non-redundant dataset. The dataset consists of 1029 B-cell epitopes obtained from Bcipep database and equally number of non-epitopes obtained randomly from Swiss-Prot database. The prediction accuracy for models based of various properties varies from 52.92% and 57.53%. Also It achived highest accuracy of 58.70% at threshold 2.38, when  combined four amino acid properties( hydrophilicity, flexibility, polarity and exposed surface).
Conformational epitopes can be predicted using DiscoTope 2.0. This method predicts discontinuous B cell epitopes from protein three dimensional structures. The method utilizes calculation of surface accessibility (estimated in terms of contact numbers) and a novel epitope propensity amino acid score. The final scores are calculated by combining the propensity scores of residues in spatial proximity and the contact numbers. Besides, Using the benchmark data set from the original DiscoTope paper, has been demonstrated that the updated method has a significantly increased predictive performance.
Important: Discotope allows to get a 3D structure of this epitopes.
I propose to use DiscoTope for prediction of discontinuous epitope residues for several reasons. First, I have shown on a data set of discontinuous epitopes that the average predictive performance of the DiscoTope is significantly higher than the Parker propensity scale and marginally higher than the surface localization score defined by the NACCESS RSA score. Second, several authors have shown that DiscoTope correctly predicts residues in epitopes that have been identified using different techniques such as phage-display, point mutation, and sequence analysis. Third, the DiscoTope prediction method is publicly available on www.cbs.dtu.dk/services/DiscoTope, and the output of the method is easily interpreted.
I would recommend you to check if this epitopes borne on the protein have possible allergenic sites that can contain experimentally proven IgE
epitope. For this you can use Algpred

Very interesting answer, but please make it clear when you are directly quoting a source.

Also note that, while you are (excellently) covering the 'how' of epitope prediction, this will not allow the OP to predict if the immune system can make antibodies against a certain protein or not (see my answer)

The answer of polonio210 is an excellent summary of bioinformatic tools, that allow comparisons with databases of known antibodies - which is helpful to find a specific antibody that could bind your protein.
It's important to note, that this approach will not allow you, to discern whether or not the human immune system will be able to make an antibody against this protein. Based on the answers & comments to this question the number of possible antibodies a single human can make ranges from $10^{12}$ to $10^{16}$. These numbers are so high, that it's likely that not database will ever be able to cover all possible antibodies and allow you to predict if the immune system could make an antibody against a specific protein.


text:
Why does my simulation not support the idea that inbreeding is bad?
After reading this post, I wrote some code to simulate inbreeding.

We have a population of $N$ creatures. Each creature has two genes, which come in two forms: recessive (a) and dominant (A). The creatures' initial genomes are random. At each stage, the following happens, in order:

Each creature with the recessive phenotype (aa) dies with probability $p_R$.
Each creature with the dominant phenotype (AA, aA, or Aa) dies with probability $p_D<p_R$.
Each creature then decides to have children with probability $q$. Each creature that decides to have children chooses a mate (see below) and has three children with that mate.

I wrote two different kinds of creature, incest-averse and incest-seking. Each time I ran the simulation, the population consisted of either all incest-averse or all invest-seeking creatures.

An incest-averse creature chooses a mate randomly and uniformly from the set of its non-siblings.
An incest-seeking creature chooses a mate randomly and uniformly from the set of its siblings. If it has no siblings, it just randomly picks anybody.

In practice, since each union produces 3 children, the incest-seeking creatures almost never fail to have siblings after a few generations.
What I found was that whichever type of creature I used, the results were the same: the frequency of the aa genotype plummeted to almost zero. I used the parameters $N=100$, $p_R=0.1$ $p_D=0.05$ $q=0.022$.
Presumably my model is in some way too simple. What am I not taking into account?
Source code

Your question title does not really fit your post. Your simulations do show that inbreeding is bad since the recessive genotype frequency drops to very low non-zero values in your inbreeding scenario, which is expected under high dominance coefficients. What does not fit your expectations is your null model: the outcome of the non-inbreeding scenario. The main problem seems to be that there is no differential fitness effect for recessive genotypes: if all recessive genotypes have such a strong negative fitness effect, you do not have power to separate your two models.

@AlexDeLarge From the reddit post I linked to, my interpretation was that reducing the frequency of aa is what we want (since that phenotype is less fit). In that case, what do we actually expect to happen under non-inbreeding, and why is it a "good" thing?

I notice your simulation doesn't actually compare the spread of phenotypes of "incest-seeking" and "incest-avoiding", you just prescribe one or the other. What your simulation shows is that deleterious phenotypes tend to go extinct, which is what we would expect, incest or no incest (if anything it might happen faster with incest because the deleterious allele is less likely to "hide behind" the non-deleterious one; see: https://en.wikipedia.org/wiki/Genetic_purging). I think the question is, what does "incest is bad" mean to you and how did you expect this simulation to show it?

Given your setting you expect to have low frequency of recessive homozygotes even without inbreeding. But in reality, recessive homozygous genotypes do not need to be deleterious, in fact only a small fraction is. Accordingly, given that recessive deleterious alleles are very rare and most often found in healthy heterozygous carriers, they are rarely combined by chance. The problem with your simulation is that it does not capture that inbreeding, due to excess homozyogotes, strongly increases that probability as you penalise every homozygous recessive genotype.

@RozennKeribin I was trying to understand why inbreeding is considered "bad", genetically. From the reddit post I linked, I thought the idea was that with inbreeding, deleterious alleles go extinct less quickly, although in retrospect that doesn't make much sense. If that's a mistake, then "Why is inbreeding bad?" should be taken to be part of the question.

inbreeding is bad becasue it prevents variety in genotype, the very thing sex evolved to produce. Sex itself is costly and time consuming so doing away with it's benefit but keeping the sex is counterproductive.

With inbreeding, you have a good chance of both parents sharing the same very deleterious mutations, which means their kids are likely to be homozygous for those mutations.  Make your sim have dozens of genes, crank up the penalties for being homozygous, and see what your populations numbers look like in the incestuous group.

I also wonder if your "sibs, then breed randomly" is going to result in a lot of outbreeding once the genetic load of deleterious mutations gets bad, and you get a lot of only children.  If you could change the sim so that singletons try to mate with cousins when there are no sibs, instead of randomly, then you'll have more inbreeding in your inbreeding population.

@Jack M "If that's a mistake, then "Why is inbreeding bad?" should be taken to be part of the question" -> it is a mistake, but given it changes the tenor of your question you might want to edit it taking the new info into account. For why inbreeding is "bad", you might want to try simulations that compare inbreeding vs outbreeding phenotypes (in the long run deleterious alleles go extinct either way, but in the meantime the inbreeders might see less-fit offspring than the outbreeders and be selected against) and asexual vs sexual reproduction (because inbreeding makes sex more like asex)

Try using nonlethal recessive alleles such as those involved in color blindness, then consider the frequency of color blindness on the two groups.

@JeppeNielsen If the alleles have no effect on death rates, then you end up with roughly 25% of each genotype no matter what. This is pretty obvious when you think about it because all four genotypes are entirely equivalent as far as the simulation is concerned.

You do certainly not get 25% of each genotype unless that is your starting frequency. Consider the case were the "a" allele have a frequency of 1% in the general population. Assume that the Hardy-Weinberg principle ( https://en.m.wikipedia.org/wiki/Hardy-Weinberg_principle) is in effect and calculate the equilibrium frequencies. Next consider the situation were inbreeding is occuring, then it should be quite clear that inbreeding increases the frequency of rare recessive allels.