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Why are livestock bad for the climate?
I have heard that eating meat is bad for our climate. This is most often explained by the following (Source):

Methane is produced when digesting food and also the faeces of cows produce greenhouse gasses afterwards
Fertilizers produce greenhouse gases
The processing of food with machines produces carbon dioxide
The farming of land with tractors etc. produces carbon dioxide

The last three points I can understand. But I have some problems understanding the first. My questions in this regard are:

Cows emit methane. But the methane is produced by digesting plants. The plants themselves got the carbon from the atmosphere. So at least this is a closed cycle and no net greenhouse gases are emitted. Aren’t livestock therefore climate-neutral?
It may be that especially for factory farming, forests are cut down. This produces a lot of carbon dioxide. But I also heard that the plants that are grown may store more carbon then the trees that were there before. Is this true? If not, is this really the only reason meat is not carbon-neutral?
How is the carbon footprint of livestock actually determined? Is it really determined by the forest which was cut down in order to produce food or is just the methane exhaust of the livestock measured?

Own research
In this source it is stated that grass-fed cows may be carbon-neutral in the long run (under optimal conditions) and may even increase carbon capture in the short run. Nevertheless, it is not explained why this is not true for crop-fed cows (how do crops and grass differ in this regard?)
On this site it is stated that “[Only] In a stable climate, trees store more carbon than grasslands”. But what about crops like wheat? They have more biomass and deeper roots than simple grasses. Also there may be several wheat plant on the area one tree takes. I found nothing regarding this on the web.
PS. I am not a biology professional so please forgive me if I misuse some terminology and do not cite scientific papers.

Short Answer
I'll address the first two of your three sub-questions:

Livestock are not climate neutral because different processes of the carbon cycle create different carbon-based molecules at different rates and that linger in various "reservoirs" throughout the globe for different lengths of time. Given these details and the fact that the underlying chemistry of the different C-based molecules varies, each carbon-based molecule has varying degrees of effect on the climate.

For example, CO2 (e.g., from decomposition of grass) has less radiative forcing than methane (CH4) (which can be created in excess by cows fed a starch-rich diet of corn).

See "Would fewer cows mean less methane emission?" for more details.

Croplands have drastically lower carbon storage ability than forests, natural grasslands, and wetlands. You can compare global measures of aboveground and belowground biomass to determine this.

The model-driven analysis of the paper your link cites is taken out of context and its comments on resiliency are not generalizable in understanding absolute carbon storage capacity. The paper comes with many caveats.

Long answer

You're inappropriately assuming that all carbon molecules are the same.

There is a finite amount of matter in the universe, including carbon. You probably know this from the Law of conservation of matter. However, one carbon-based molecule does not necessarily (and in fact does not) have the same physical and chemical characteristics of other dissimilar carbon-based molecules.

Importantly, not all carbon-based molecules are greenhouse gasses, which have unique reactivity and physical structure to function as re-emitters of infrared radiation. See here for an explanation and here for a simplified YouTube video cartoon explanation by "Minute Earth".

Carbon returns to the atmosphere typically via combustion or decomposition. (See comments about the carbon cycle below). Much of the carbon released by these processes are either CO2 or CH4.

The carbon cycle reflects the law of conservation of matter in the recognition that carbon transfers from one object to another via biogeochemical cycling; however, how it transfers varies both in the chemical and physical processes occurring, in the time spent in one "place" (i.e., a nutrient/chemical "reservoir") vs another, and in how readily it "comes"/"goes" from one place to another (i.e., its flux rate).

The timing of residence times and flux rates (i.e., movement from one place to another) dictate whether a reservoir acts as a source or sink.

CO2 (carbon dioxide) and CH4 (methane) are quite different in the reactions from which they are generated (see Would fewer cows mean less methane emission?), the rate at which they are generated, and ultimately in their chemistry. This last point has drastic impacts on residence times, flux rates, and ultimately their climate warming impacts:

Both molecules differ in their residence times in the atmosphere as well as their magnitude of radiative forcing. From MIT:

methane immediately begins to trap a lot of heat—at least 100 times as much as the CO2. But the methane starts to break down and leave the atmosphere relatively quickly. As more time goes by, and as more of that original ton of methane disappears, the steady warming effect of the CO2 slowly closes the gap. Over 20 years, the methane would trap about 80 times as much heat as the CO2. Over 100 years, that original ton of methane would trap about 25 times as much heat as the ton of CO2.

Note, also, that some of the atmospheric methane will eventually be chemically converted to carbon dioxide. From here.

Methane enters the atmosphere and eventually combines with oxygen (oxidizes) to form more CO2. Methane converts to CO2 by this simple chemical reaction.

Regarding methane production of cows and rates of release of greenhouse gasses, please see my other recently-answered BIO.SE post: Would fewer cows mean less methane emission?
2.Regarding carbon storage:
As stated above, understanding the carbon cycle requires both an understanding of residence times and flux rates. To determine the carbon storage ability of one biome or environment vs another, we typically measure the biomass of the organic matter (with interest in determining the C:N ratio) as well as flux rates in/out of our target carbon reservoir (e.g., plants such as crops or trees). Regarding flux rates, of particular interest are rates of carbon sequestration.
Ultimately, any community of plants that is capable of sequestering more carbon into large amounts of high-C:N biomass will result in larger carbon storage. The longer-lived those plants (i.e., the less labile their carbon), the longer that community of plants acts as a carbon sink.
- Also note, that different climatic conditions (e.g., see [Gallardo & Merino 1993](https://doi.org/10.2307/1939510)), plant-cell chemistry (e.g., C:N ratio as well as % of [lignin](https://en.wikipedia.org/wiki/Lignin); again see [Gallardo & Merino 1993](https://doi.org/10.2307/1939510)), plant anatomy (especially root structure; see [Poeplau et al. 2021](https://pubmed.ncbi.nlm.nih.gov/34228862/)), plant age (e.g., see [Peichl & Arain 2006](https://www.sciencedirect.com/science/article/pii/S0168192306002188)), and plant diversity (see [Chen et al. 2018](https://www.pnas.org/doi/10.1073/pnas.1700298114)), etc. can impact the degree of carbon storage in the organic matter of soil: [soil organic carbon](https://www.agric.wa.gov.au/measuring-and-assessing-soils/what-soil-organic-carbon).

So two questions of interest are:
 - **which plant communities store the greatest amount of carbon-rich (i.e., *woody*) biomass in the smallest area (or volume) of space for the longest amount of time?**

 - **Which plant communities have the least disturbed (least labile) organic matter sinks**?

We can approach this in two ways: per area or across the globe:

Across the globe: see here, here, and here for depictions and explanations. Many have tried to quantify this, so various values show up. Below are some examples:

 Carbon (Gt C) stored in ecosystems (based on Scharlemann et al., 2014); source: U.S. Forest Service

 Source: IPCC

Per area:

 Source: FAO
If we take the carbon mass numbers from the IPCC table in the section above and divide by total area, we can get estimates of total biomass. visual Capitalist did so conveniently, which I copy below:

 Source: Visual Capitalist; original data from IPCC 2000
Do note, however, that the per-area storage of carbon of any one of these biomes (especially forests) would be greatly impacted by the age of a given patch of vegetation. As such, the numbers in the above table only reflect current biome statuses vs maximum storage of these plant communities under ideal (i.e., non-anthropogenically degraded) conditions.  Of particular note, is that temperate forests vary greatly in their biomass based on the age of the stand: old-growth forests have much greater biomass per hectare than secondary forests or managed forests. However, the majority of temperate forest land (i.e., the numbers captured in the table above) currently is managed or secondary in nature and therefore does not fully capture the carbon storage ability of less-anthropogenically-modified versions of temperate forests. This explains why these numbers are much lower than other forest types.

Some estimate that <10% of forests in the US (as low as 1%, see Davis 1996's Old growth in the East: a survey), are old-growth in status. (You can ignore references (e.g., here) to studies like DellaSala et al. 2022 which show much higher numbers because they are defining mature forests as 80 years or older -- hundreds of years younger than is typically used to define old-growth status and certainly nowhere near even the transition point of many temperate forests).

Also note, that total carbon currently sequestered vs. rate of sequestration are different. Large woody biomass is a huge sink of carbon but not necessarily quicker at sequestering new carbon. For example, see Heinrich et al 2021 ("Tropical secondary forests sequester carbon up to 20 times faster than old-growth forests").

Croplands (especially those managed by modern high-throughput industrialized agricultural practices) are constantly losing organic matter in soil due to tilling, erosion, etc. Undisturbed forests essentially have little to know organic matter loss (though this depends on climate and local hydrologic cycling).
Your reference to grasslands being better carbon sinks vs. forests is taken out of context (or at least inappropriately generalized). The study (Dass et al., 2018) out of UC Davis -- influenced by the propensity for large California wildfires due to years of fuel buildup negating their typical long-term storage ability -- used a set of models to predict future change. I'll leave it to you to read the actual paper, but at the core of their claims is that "extreme heat-waves, drought and wildfire have increased tree mortality" in California while grasslands are more resilient to these issues given their propensity to store most of their carbon underground. they built their models assuming these risks continue, and thus claim that grasslands are more resilient carbon sinks in the state of California.

From their conclusion: "Our study demonstrates that, in the absence of aggressive mitigation of global greenhouse gases, forest management strategies to reduce fire risks, or both, grasslands will store more C for a longer period of time than forests in California." they also note that their results reflect "dryland" forests, but as we can see above, most of the carbon is stored in tropical and boreal forests as well as wetlands. They also note: "our results indicate the potential direction of change as opposed to predictions that consider the full ensemble of ecological, physiological and management factors that can alter pathways and responses of ecosystems to climate change."

In other words, their model-based prediction study is not meant to be a generalizable nor understood-to-be-factual study, but another piece of thought for California policy-makers...

Short answer
Two factors playing a role in livestock's contribution to the greenhouse effect have to do with methane being a more potent greenhouse gas and the fact that the conversion of plant materials into meat comes with low efficiency.
Background
Up front - I'm not a climatologist. My 2 cents worth here are two points:

Methane is a potent greenhouse gas, and way more potent than CO2. Quoted from UN Environment Programme's website:

Methane is [...] a powerful greenhouse gas. Over a 20-year period, it is 80 times more potent at warming than carbon dioxide. Methane has accounted for roughly 30 per cent of global warming since pre-industrial times and is proliferating faster than at any other time since record keeping began in the 1980s.

and

Livestock emissions [...] account for roughly 32 per cent of human-caused methane emissions.

Another issue is the food pyramid, which consists of different layers: organisms higher up in the food chain consume biomatter from lower layers. Every layer dissipates heat, because of efficiency being less than 100% (Fig. 1). Often live stock is fed on crops specifically produced for the meat sector. If the production of all this animal fodder would instead have put to use to grow veggies for human consumption, a lot more food would have been available than when it is inefficiently cycled through live stock first to turn it into meat (and methane).

Fig. 1. Transfer of energy through an ecosystem. At each trophic level only a small proportion of energy (approximately 10 percent) is transferred to the next level. source: Encyclopædia Britannica

I have found an answer for your first question. The Global Warming Potential of methane is much higher than that of carbon dioxide. Because methane stays in the air for a shorter period of time than carbon dioxide, the GWP is higher for a shorter period of time: over 20 years it is approximately a factor 70. In 100 years the factor is approximately 30. And in 500 years, methane has still 7 times higher warming potential.
Note that the GWP compares the warming potential of one tonne. If we assume that one mole of carbon dioxide is converted to one mole of methane (since both contain one C atom), then it follows that 1 tonne becomes 0.36 tonnes. This follows from comparing the molar mass of carbon dioxide and methane. Taking this into account, it would still be better if carbon dioxide is not converted to methane.
Therefore, a closed cycle which converts carbon dioxide to methane contributes to the greenhouse effect.


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CSF types in humans
There are several blood types such as A, B and O. Crossing these blood types such as in a transfusion, the results can be fatal. Along these lines, issues can arise when an organ or bone marrow are placed in a new host, issues can arise if certain markers aren't met.
With these examples in mind, are there multiples types of CerebroSpinal Fluid (CSF)?
In attempting to research this subject, I did not find anything answering this question, included is an article discussing CSF, but not mentioning different types of CSF. Science Direct Article on CSF

https://biology.stackexchange.com/q/94/5198

@David: Thanks for the edit.

source: Stack Exchange

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sort: votes


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Meaning of PAM matrix values
If PAM-1 matrix refers to time or evolutionary event for 1% change in amino acid sequence of a protein then how come there is PAM250? shouldn't PAM 100 be the highest where the two concerned sequences are 100% different

What attempt have you made to find the answer to this frequently asked question on line? Please read the help on asking good questions. Tell us what pages you have consulted and why you do not understand the explanation. Then we can help.

I used Xiong's and Jhumur Ghosh's bioinformatics books. they both explain how the matrix are made pretty well but my confusion is what I stated in my question. Page 148 Jhumur Ghosh's book states that the PAM 100 matrix corresponds to 100 accepted mutations per 100 residue. So, shouldn't it be the highest available matrix where the entire sequence is different. it clearly states there is 100% change in 100 amino acids after all. but then it also states one residues can also change more than once. how come one single residue can change multiple times when I am comparing two sequences only.

English is not my first language, so, may be a little different set of words might be helpful for me to understand what really is going on. that's all

No. The terminology is difficult even for English native speakers. The key is what an “accepted” mutation is. Try Wikipedia or other sources that explain that. I’m on vacation so can’t actually check. Search for “accepted point mutation” perhaps.

Accepted mutations are those that are accepted by nature, for example a hydrophobic amino acid substituted by another similar hydrophobic aa which does not negatively hamper with the protein structure and thus naturally selected. Any lethal mutations or silent mutations won't be part of accepted mutation.

No. Not in this context. Do as I say and search.

https://en.m.wikipedia.org/wiki/Point_accepted_mutation?wprov=sfla1

Let us continue this discussion in chat.

You misunderstood slightly what PAM1 means; it's actually (from Wikipedia) "1 [PAM] mutation to occur per 100 amino acids". So PAMn makes sense for any n, as in the 100 amino acids may mutate more than once each, on average.
Or if you put it in terms of PAM distance...

Is possible for two sequences to be more than 100 PAM
  apart?
  Yes: One position can mutate multiple times.

An attempted analogy: what does 600% casualty rate (for soldiers) mean? Well it means not only the original guy died, but his 5 replacements got (successively) killed as well.

If I am dealing with multiple sequences it makes sense if one position is getting mutated time and again but if I am comparing only two then how come one position is mutating multiple times?

For example, if the query is MFPIMW and the sequence I am trying to align is MWPIMW then one spot at F is mutated, how can this specific spot mutate twice when I am dealing with only these two sequences.

@Anindya: it can because a PAM is not a simple mutation. Given two randomly chosen amino acids, you may not have a PAM of 1 between them. Look at PAM1 for instance; note that the matrix entries are probabilities multiplied by 10,000 in there, i.e. the actual numbers are less than 1.

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Anomaly in growth of fungus in Potato dextrose broth.. turbidity is not seen in one flask
I have inoculated six flasks of 200 ml potato dextrose broth, one of which does not show any turbidity and the medium is clear with a fungal disc in it.
All were inoculated at the same time and from the same pure fungus culture.
What might be the reason for this anomaly?

Several explanations are conceivable. Knowing what type of fungus you are working with and how exactly you proceeded to inoculate the cultures could help narrowing down the possibilities.
Here are some possible explanations:

Since you inoculated six liquid cultures from the same stock culture, the process might have been too long. Let me explain. Most fungi are strictly aerobes and do not tolerate well even short lack of oxygen. So, as I can guess, while you were inoculating the dextrose broths one after the other, the stock culture just remained unaerated on your bench. Since it can take a few tens of minutes to prepare everything and to proceed to the inoculations, it is possible that while you were doing so, the physiological state of the fungi just kept deteriorating, to such a point that one of the last inoculations did not contain enough viable cells to initiate a growth in the broth.
You might have forgotten to shake the stock culture just before taking the sample used in order to inoculate the broth. So it is possible that all the biomass in the stock culture was sedimented and you just inoculated your broth with the supernatent.
Also, a classic mistake is to mix up some of your broths. You think that you have inoculated all six broths with the stock culture, but maybe you unintentionally skiped one, or maybe you inoculated the same broth twice.

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Actual determination of the DNA sequence in the shotgun approach?
I'm studying bioinformatics and I'm confused by shotgun sequencing. In Sanger sequencing we break up the DNA and use ddNTPs in order to determine the exact position of each neucleotide. How exactly does shotgun sequencing help us determine the sequence structure?
If we break up the sequence randomly and then stitch it back together by looking at the overlapping parts, how does that tell us what order the nucleotides are in? How exactly are the nucleotides read so that shotgun sequencing helps us?

The wiki page seems to provide a simplified schematic (the first table and accompanying text). What is not clear to you exactly?

@AliceD Basically, I'm under the impression that sanger sequencing isn't used in cases for very long DNA strands. Shotgun sequencing works better here but I'm not sure how shotgun sequencing accomplishes the same thing that sanger sequencing does? Sanger sequencing tells me the position of the nucleotides and therefore the structure of the DNA strand. How does shotgun sequencing do this?

Fair enough I guess. I'll leave this one up to our molecular biologists to assess. I held my last pipette back in 2001 O.o  Auch, I'm getting old

Does this answer your question?

@AliceD Not exactly. I appreciate you taking the time to search for things though. The only thing that makes sense to me is that the shotgun sequencing involves breaking up the dna strands that are too long, performing sanger sequencing on them, and then looking at overlap. But it doesn't seem to say that on the Wiki, and it says a LOT of other stuff that I don't relaly understand what it's for.

Would it answer your question if I said that shotgun sequencing isn't actually a sequencing technique, per se, but a method of assembling a large number of short sequence reads generated by Sanger sequencing? In other words, to sequence long DNA molecules, you would break it down into short fragments that Sanger sequencing can handle and then reassemble the reads based on overlapping nucleotide sequence.

I have modified the emphasis of the title seemed to be on assembly which did not reflect the question. The poster appears to know about computer assembly of sequenced fragments, what he appears unclear about is how the identity and order of the bases in the fragments are determined before this reassembly. (Or perhaps he thought it was part of the reassembly process, but in any case it is this determination that he is unclear about.)

@David Great, thanks a lot. There was a lot of things that I was confused about not having a background in biology but this has helped tremendously. The title does better reflect what I was after.

The question appears to confuse the method of identifying and determining the order of bases in a fragment of DNA — Sanger* sequencing, Maxam–Gilbert or more modern ‘next generation’ methods — with the strategy for selecting fragments to analyse and reassemble into the larger contiguous sequence from which they were derived, of which shotgun sequencing is one.
Shotgun sequencing is a strategy in which the selection of fragments to sequence is random, the method of sequencing is a matter of choice (it was often the Sanger method when it was first developed), and the assembly is done by computer programs that identify matching stretches. (It fails — or is not completely successful — if by chance the fragments do not cover the whole DNA with suitable overlaps or there are certain types of repeated regions.)
Shotgun sequencing should be contrasted with what might be called ordered sequencing strategies in which one generally starts with a restriction map of the whole DNA and initially selects specific fragments to clone and sequence (by whatever method seems best). On the basis of the sequence of the fragment one can choose to sequence further from a position within the already sequenced fragment, and this procedure repeated. Here there is no apparent assembly step as this is inherent in the choice of fragments to sequence. (This is much slower than shotgun sequencing, and cannot be automated so that it is much more expensive. However, it is more precise.)
Coda
Part of the confusion may arise from the fact that modern automated methods of sequencing genomes are designed to work on a mixture of many uncloned fragments of DNA, so inherently involve the shotgun sequencing strategy. They tend to employ technologies other than the classic Sanger method. If a ‘manual’ clone-based ordered sequencing strategy is required to ‘finish’ missing or ambiguous regions of a genome, this would most employ the Sanger method of determining the sequence. Hence, the contemporary writer might employ what is, in fact, a misleading contrast.
*Fred Sanger was an eminent Nobel laureate, so his surname is capitalized.

I hope this is clear. I can add a diagram if necessary.

This is clear! Thank you for explaining. Would it still be possible for you to provide a diagram as they usually drastically improve my understanding.

In Sanger sequencing we break up the DNA and use ddNTPs in order to
  determine the exact position of each neucleotide.

No.  Sanger sequencing doesn't do this.  The results of one Sanger sequencing reaction is a string of nucleotides, about 700-1200 bp long.  There is nothing in that which inherently gives that string a position.
"Shotgun" just means that you aren't take advantage of any kind of known mapping information to target your sequencing reactions; you sequence everything randomly, and let a computer sort out what overlaps with what.

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Is most of the human genome functionless “junk DNA”?
In January 2012, David Icke published a book (ISBN: 9780955997334) entitled “Remember where you are and where you come from” in which he challenged what he claimed to be the view of mainstream science that 90–97% of the human genome was “junk DNA”, serving no function. He implied, instead, that it must have a function, but that this was unknown.
Is it still true that we do not know what all this DNA does? I see that we consider this DNA to be non-coding, but does that mean it is “junk”? I find it hard to believe that it can serve no function, otherwise why would the DNA be there? Is it possible that it is used for things we don't yet understand?

This question contains more info on what non-coding DNA is, but I think Remi has answered whether or not Icke's claim is right.

@David that's reasonable, but i voted to leave this open and downvoted. I think the reference to Icke's book as the thing that sparked the question, and the actual question (what is junk DNA and do we know what it does) is on topic (general questions about biological concepts). The question could be improved by removing the reference to the book by a professional conspiracy theorist, since it distracts from the actual question about biology.

I’d check whether there are any other questions on junk DNA. Otherwise edit the question drastically so that it deserves an answer.

"Junk DNA" is no longer used. This term originated a long time back when the function of the non-genic/intergenic DNA was not known. I'm not sure which "mainstream science" is he talking about!

I couldn't find a suitable previous question on junk DNA so I have rewritten the question. I would suggest answers address what has been discovered in the last seven years since the book was written.

I'm going to urge people not to respond to this unless they are actually working in the field. I don't know of any field in science to which the Dunning-Kruger effect applies more. If you are confident you understand this field, you almost certainly do not. There is a large and highly focused literature on this, and almost no one outside the field even knows the field exists, let alone has read any of the papers in it. If you have not read at least 100 papers specifically on the topic, your answer will be wrong and misleading.

@David I think your edit to the title implies that it was once thought that "junk DNA" is functionless; it's possible that's the case, but not to my knowledge. Unless you have a reference that in fact junk DNA was thought to be functionless at some point, I think the previous edited title "Does "junk DNA" serve no function?" is much better.

@BryanKrause — I think it better not to use a form of words that implies acceptance of the term. How about "Has most of human DNA no function?" and reference the following: http://www.junkdna.com/ohno.html?

@David What do you think of my compromise edit to the title? I think it's roughly between what each of us are suggesting.

@BryanKrause Fine. I'll add a link to the Ohno paper etc. in the question to give it a little context.

What is junk DNA?
The term junk DNA is not used that often in the scientific literature and when it is it is often used very generally, often early in the introduction. It generally refers to any non-coding DNA.
In humans, about 25% of the non-coding DNA is introns and regulatory sequences. These sequences are highly essential for the working of the organism. There are many cases of adaptation from these regulatory sequences (see this answer).
The term junk DNA is very loaded and may make it feel to people that this DNA is not important for the organism survival but this is not quite what was first meant by the term junk DNA. It is true though that repeated DNA such as those in  transposable elements are thought to have little impact on the organism phenotype. Transposable elements can however have important role on the evolution of a lineage.
IMO, the claim is false and insulting
By saying things like They do this because they gave no idea what it does and, from their version of reality, it appears to serve no function., it feels to me that David Icke is using the loaded side of the term junk DNA to insult all geneticist in general.
D. Icke is 1) doing a strawman by suggesting that geneticists think that regulatory sequences are of no use and 2) he is suggesting that geneticists are biased and will invent whatever theory in order to match with a pre-conceived opinion of the reality.
About David Icke
I don't mean to make an intentional fallacy but I would like to note that David Icke is a famous conspiracy theorist who has been illogical and obviously opinion based many times. For example David Icke claims that the moon is actually a spaceship and not a natural satellite (see here). He has made many other fantastic claims of the kind. Scroll down the wikipedia article to enjoy some non-sense!

I know a lot about Icke's material. Some is spot on and some is sketchy, but I don't think ad hominem ever discredits an argument so it's probably best to removed the last paragraph.

You say it's 5-10% that's regulatory in the other answer, which I think is more accurate

The term "junk DNA" is not commonly used any more by scientists. It became popular when people realized, that only 1-2% of the human genome encode proteins, and wondered about why there is so much more DNA if it's not needed. But we know today, that it does in fact serve many functions and therefore is now referred to as "non-coding DNA".
Some non-coding DNA functions:

regulatory elements: promoters, enhancers or silencers are DNA regions, where transcription or other binding factors bind to DNA to regulate the accessibility of genes to the transcription machinery and therefore control which genes are expressed
introns: DNA regions that are inserted into the actual coding region and removed during splicing. They serve a role in RNA processing and alternative splicing.
functional RNA: Not being translated into a protein doesn't mean that the RNA produced by a locus doesn't serve a function in the cell (e.g. ribosomal RNAs, microRNAs)
structural elements: telomeres and centromeres are important for chromosome stability, sister chromatid linkage, heterochromatin formation and anchoring to the nuclear envelope

We keep learning more and more about different functions of DNA regions. Even open reading frames (ORFs), which encode for functional RNAs or even small proteins keep being identified. It's therefore not true that it does not serve any function, because we have identified many functions. And while we still don't know everything about it, our knowledge is increasing.
Further reading:
Shanmugam et al. 2017 - Non-coding DNA – a brief review
NIH Genetic Home Reference - What is non-coding DNA?
Wikipedia - Non-coding DNA

How much of the 90-97% do you think the points you mention cover? The only point that is really new this century is "functional RNA". It may be true that "we keep learning more", but that hardly answers the question.

On the other hand large segments of non-coding DNA have been removed from mice with no apparent affect on their phenotype. It's a complex topic that is far from settled.

@David: The question was if if non-coding DNA is junk and has no function as put forward by the quote from David Icke that you edited out of the question, which also implied that scientists don't seem to be interested in it, just calling it junk. That's not true, since we have discovered functions for a number of non-coding elements. There might be even more that we haven't figured out yet. Effects might be less direct (e.g. evolutionary, as mentioned in the answer by Remi.b), but scientist keep working on it.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/


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Anatomical separation of body components
What separates the organs and parts of the body, for example, the intestine and the spine?

This image shows what makes this separation, but what would be represented in orange and yellow?

In vertebrates at least, organs are contained within body cavities, delimited by serous membranes. Here you seem to be pointing at the limit between the abdominal body cavity (delimited by the peritoneum) and the spinal body cavity (delimited by the meninges).
Take a look at the Wikipedia page (and related links):
https://en.wikipedia.org/wiki/Body_cavity

I imagined it would be the peritoneum, but in the image I sent, it wasn't evident, thank you very much!


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Effect of ethanol on TRizol RNA extraction
I added ethanol instead of chloroform to the cell suspension in Trizol. Can I still obtain my aqueous phase?

How much ethanol did you add?

I added 100 uL of etanol

To which amount of sample?

to 500 uL of cell suspension in Trizol

@polonio210 Can you edit that information in the comments into the body of your question?

My answer is based on my experience in the lab and something like a best guess - it may or may not work. But given the fact that added 100µl of ethanol to 500µl of total volume and since water and ethanol mix completely, I would give it a shot.
I don't think that the ethanol would change the polarity of the solution so much that phase separation is inhibited. The only thing that I can image is the contamination of the aqueous phase with traces of phenol, so I would probably clean up more carefully and do an additional NaOAC/ethanol precipitation at the end of the procedure. If you expect a small pellet with little nucleic acids, add some glycogen to get a better outcome there. I would appreciate it, if you could comment on your experience (and the outcome) when you try to save you sample.

Thanks Chris, Oh yes, I will let you know!


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Klenow fragment does not seem to have 5->3 exonuclease activity, but it can still displace nucleotides in front of him - How?
Klenow fragment does not seem to have 5->3 exonuclease activity, but it can still displace nucleotides in front of him - How? How would this displacement mechanism differ. My first guess is that exonuclease activity actually digests upcomming strand into single nucleotides, but how come the displacement activity not get in the way for lab work? :
"The 5' -> 3' exonuclease activity of E. coli's DNA polymerase I makes it unsuitable for many applications. "

Why doesn't the 5->3' displacement activity make the applications troublesome then? What would those applications be.
I've spend a long time looking for these answers, but unfortunately I've found nothing.
Maybe someone has any idea:)
Cheers!
References:
Image - http://www.vivo.colostate.edu/hbooks/genetics/biotech/enzymes/klenow.html

Welcome to Biology.SE. Please provide references to images you add to your posts.

Generally, the New England Biolabs website is a great resource for this sort of information.  Maybe you already know this: Klenow fragment is widely used in molecular biology today. The broad use of Klenow fragment is because it will remove 3' overhangs, thereby 'polishing' or 'blunting' the DNA.  See the famous cloning techniques manual for additional information.
It is a polymerase, though, and it does perform 5-->3' elongation in the presence of dNTPs.  (sidenote: Klenow was initially used in polymerase chain reaction (PCR) development, and later replaced with heat-stable Taq pol.)
The so-called 'strand displacement' activity of the enzyme allows the 5-->3 elongation of the new strand to occur even in the presence of an existing, annealed strand ahead of the advancing polymerase, as you say.  This may seem problematic at first glance, but the job of polymerase is to make a complete, templated copy of DNA -- that is why reseachers use it, and that is its job in nature too!  Stand displacement is really convenient for scientists when using random primers, for instance.  The DNA polymerization can continue unimpeded despite the presence of a 'downstream' barrier.  This is also why not having 5'-->3' exonuclease activity is helpful in this context.  (sidenote: pol I is not the main replicative polymerase in E. coli. and its discovery is one of the great stories of post-war biology).
I hope this addresses your question(s).

Thank you for your answer. I am still unclear on one point - how is strand displacement activity different from 5->3 exonuclease activity. They both remove nucleotides in 5->3 direction, don't they?

a nuclease digests DNA; strand displacement is not strand digestion


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Can you identify this wasp-like insect?
I've never seen anything like it, although I suppose it could be a wasp or an ant with wasp-like colour bands. Found in our garden today (Cambridge, UK). It's about 1.5 cm (half an inch) long.

Thanks!

It looks like the parasitic wasp, Ichneumon stramentor, as found by my amazing girlfriend, and discussed on Nature Spot (UK). And it's a female to be even more precise:

Description: Length 13 to18 mm. Female - Long tapered abdomen, first half yellow and rear half black, with yellow spot at the tip (both on the top and beneath. Legs have black femora; tibiae are half yellow blending into brown that exceeds to the tarsi. Black thorax (with yellow spot) and black head. Long dark antennae with broad white patch about half way along its length. Wings have a brownish tinge. Male has all dark antennae, no yellow spot to the tip of the abdomen. (emphasis mine)

It can be seen from April to July, commonly in meadows, hedgerows and woodland edge.
The adult wasp lays its eggs inside caterpillars which, after hatching,  eats the caterpillar from the inside. Hence the "parasitic" descriptor.
Further reading at Paul's Back Garden Safari
Wiki article on Ichneumonoidea

We're looking for long answers that provide some explanation and context. Don't just give a one-line answer; explain why your answer is right, ideally with citations. Answers that don't include explanations may be removed. Besides it is good to avoid writing personal information in your posts in both question and answer on the main site.

@qris: Sanjukta is right: please add some info from one or more (reputable) source(s) providing a bit more support for your answer. We like to differentiate ourselves from most sources of species ID by providing  detailed and referenced answers.... Other than that, awesome find by your girlfriend -- wasps are not easy to ID!! :D.

Qris, I took the liberty to edit your post to bring it within site guidelines. If the edit is unacceptable in any way, please feel free to roll back. Good find!


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Cicada Killer Behavior
I've had a giant wasp hanging around outside my window the past few days, so I've resolved to learn more about it. I believe it is a male Cicada Killer, because it displays the following behavior:

During the day, it is extremely localized in a region less than a square meter.
It lands or hovers in the same grassy area all day, and occasionally chases off other wasps that come near it.

First question: Am I correct that this is a male? The females should be off burrowing or catching Cicadas, right? He is quite large (2 inches?), but I don't have a female for comparison in terms of morphology.
Second question: Where does this guy go at night? He leaves before sunset (~5 pm) and shows up again in the morning (~10 am).
Third: If he's around, I should be able to find some female burrows in the area as well, right? Where should I look for these for confirmation?
The question is admittedly a little vague since I am just trying to confirm I understand the behavior I am observing, but I've tried to isolate the specific questions I want answered.
EDIT: Finally got some pictures, only these two came out.

Can you post any images?

Yes, it's a male.
http://bugmugs.org/wordpress/wp-content/uploads/2012/08/cicada_killer_pair_00052.jpg
Source: http://bugmugs.org/2012/08/cicada-killer-pair/
Update:
Wasps are in general very territorial. Even a paper bag can scare them as they take it as enemy hive. More on this: Do fake wasp nests actually fool wasps?

Where does this guy go at night?

Wasps are known to be lazy(less active) at night. Probably they go to the nearby mud nest.

If he's around, I should be able to find some female burrows in the area as well, right?

yes, there are chances of finding a female burrow near by, as they rarely fly away farther than the nest. Otherwise, there main food(cicada) is very heavy for them to carry to the nest.
follow this if you want to find it's borrow: http://www.wikihow.com/Get-Rid-of-Ground-Digger-Wasps-(Cicada-Killers)-from-Your-Lawn

It is extremely difficult to get close to this guy to check, but 1) I don't see a stinger, 2) cannot confirm or deny spurs, and 3) doesn't appear to have the "fuzzy" thorax. But man this guy is big - does the extremely territorial behavior match the female?


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How hard would it be to create a protein "by chance"?
I just read an article about David Gelernter, who was arguing against Darwin's theory of Natural Selection. He said one particular thing which stood out to me:
"...how hard it would be to create just one new protein by chance — the odds are so astronomical that there are fewer atoms in the entire universe in comparison: “The odds bury you. It can’t be done.”
I'm wondering how one could back up this idea. My back of the envelope (not being a biologist...) would go something like this:
Protiens are made of amino acids. Amino acids are essentially made up of four things, C, H, O, and N. In order to "make" amino acids, I just gotta give these things the right energy so they can strip some electrons and hook up to each other. If want to make all amino acids with say 20 molecules, I get four choices for each of twenty things, or $4^{20}\sim 10^{12}$ possible amino acids. Wikipedia tells me "most proteins are built from up to 20 different amino acids", so how many proteins are there made up to 20 amino acids?
$$(10^{12})^{20}\sim 10^{240}$$
So ignoring overcounting and how stupid this estimate is, that's a big number. And indeed, that's bigger then the number of atoms in the universe (like $10^{80}$ by some estimates).
Can someone confirm that's how he arrived at that estimate?
NOTE: Careful, I am not trying to get into an argument about Darwin - I only want to know how people who use this argument, make this argument.

It's a ridiculous statement, so you'd have to ask him how he arrived at it.

Sounded like an argument he was referring to though, right? It's true, if this is just him I'm asking a pointless question.

@cduston It's a bit like if you told someone that you walked to work, and they started telling you about how impossible it is to teleport from home to work. It kind of doesn't matter how they got their numbers about how improbable teleportation of an intact human being is, once they've refused to accept that you accomplished this by walking, the details of their alternative explanation don't really matter.

I don't wish to appear to be answering this question in a comment, and I have the feeling that it has been asked before, but if it hasn't anyone is welcome to expand on the following thoughts. 1. This is a common statistical fallacy. You have to ask what false assumptions are being made. What does creating a protein by chance actually mean? 2. The evidence says that it is possible to create a catalytic active molecule by 'chance' by the aptamer selection experiments. Lots of them. Just like there are lots of polyclonal antibodies against the same epitope. So how ever clever the arguments...

@David: I agree with everything you've said, but it wouldn't count as an answer because it doesn't address what assumptions he's using. I'm essentially assuming that "picking" means "combining", but of course there's a lot of missing chemistry there. Can you add more reasonable mechanics and still get the same argument?

@Cell: I asked here because I want to see if this argument can be made with some biology and chemistry principles. If so, it would give the argument more weight. For example, if I ran a simulation for 13.7 Gyr and didn't randomly produce any amino acids, the argument would be somewhat more valid. I'm asking if there is anything to be found of that nature in these arguments.

@cduston It's probably better to explore the abiogenesis tag to look at ways that people have studied creation of biologically-relevant molecules before biology, rather than starting from a nonsense argument.

David is right, this question (more generally) has been asked before  on skeptics https://skeptics.stackexchange.com/questions/32283/are-the-outcomes-of-evolution-too-improbable-to-have-occurred-in-the-earths-lif/32286#32286

I'm not trying to answer the question: I'm saying that this is a conjouring trick. You are so busy following this calculation that you don't question its relevence to biology, even though from your experience you know that it is a trick. You have been tricked into accepting a deliberately vague false premise of the sort that evolution requires the chance formation from scratch of one specific 100-amino acid protein. We all enjoy being tricked by a good conjourer, but we don't go away believing in magic, do we?

Why would a protein have to form on its own? proteins in life are constructed by nucleic acids,  we already know RNA can occur by chance.

In the original column for The Claremont Review of Books, David Gelertner does not suggest starting from atoms, but from amino acids. This changes the calculation slightly:

The total count of possible 150-link chains, where each link is chosen separately from 20 amino acids, is 20^150. In other words, many. 20^150 roughly equals 10^195, and there are only 10^80 atoms in the universe.

In any case, these kinds of estimates are purely theoretical and are not hugely useful. We do not know how early proteins evolved, but they did not have to just assemble from scratch.

As mentioned in the comments, this kind of argument for creationism (or 'Intelligent Design') is like a card trick - you start by dazzling with vast numbers, and use them to conceal the logical sleight of hand.
The premise of his argument is simple - there are a vast number of possible sequences, only a small fraction of those can fold into functional proteins, and there have not been enough mutations to make up the difference.
There is this strange argument:

But what does generating new forms of life entail? Many biologists agree that generating a new shape of protein is the essence of it

I'm not sure who these 'many biologists' are, but the relationship between novel folds and new species is not clear to me, at least.
Anyway, the second part of his argument relies on the work by Douglas Axe on estimating the fraction of functional folds (see this paper for example). Although he describes him a bit oddly ("Axe is a distinguished biologist with five-star breeding") it's reasonable to make this kind of estimate.

He estimated that, of all 150-link amino acid sequences, 1 in 10^74 will be capable of folding into a stable protein. To say that your chances are 1 in 10^74 is no different, in practice, from saying that they are zero. It’s not surprising that your chances of hitting a stable protein that performs some useful function, and might therefore play a part in evolution, are even smaller. Axe puts them at 1 in 10^77.

So here is the very small number to contrast with the very large one of the first step. Now for the 'bridge' - the large number of attempts that would be necessary to make a very rare event (a folded, functional protein) possible.

Suppose, then, that every bacterium that has ever lived contributes one mutation before its demise to the history of life. This is a generous assumption; most bacteria pass on their genetic information unchanged, unmutated. Mutations are the exception. In any case, there have evidently been, in the whole history of life, around 10^40 bacteria—yielding around 1040 mutations under Axe’s assumptions.

So the argument - roughly - is that 10^-77 * 10^40 is still very small. That is, mutations are not frequent enough to overcome the extreme rarity of functional sequences.
The sleight of hand, I think, is to confuse abiogenesis and mutation. When talking about the entire 'landscape' of possible sequences we are talking about abiogenesis - randomly picking 150 amino acids (say) from an alphabet of 20. When talking about bacteria we are obviously talking about mutation.
We really have no idea how the first primordial proteins formed, or what their properties were. They could have used a smaller set of amino acids (although this does not change the numbers much), or could have assembled from multiple smaller peptides, or even been partially folded.
On the other hand, mutation of existing proteins necessarily happens on sequences that can already fold. Moving to a sequence that is a neighbour in fold space is very different to picking a completely new point in that space.
So really, the numbers do not tell us anything because they relate to separate questions.

But what have the number of atoms in the universe to do with anything? It implies that every possible protein would need to be made to get one that did the trick and that’s what evolution assumes and that’s impossible. You’re looking where the conman wants you to look, and not noticing what he’s doing with the cards.

This is the answer - if we can get a citation for the quote I'll mark it as such.

@David: again, I explicitly asked to not look at the cards. I wanted to know if the calculation involved anything except for a basic understanding of chemistry and probability, and apparently that is all. It's also enough for us to know how much worth to assign to it.

When talking about abiogenesis it's also worth to mention that modern life uses 20 (actually 21-22) aminoacids - we don't know how many it were initially but it's pretty clear that starting number of amino acids was smaller (i.e. more common & simple aa's like glycine and alanine have more triplet codons). This can change the number of possible combinations by several orders of magnitude

@Nicolai - That's what I meant by "restricted set of amino acids", I'll make that clearer. However it doesn't make much difference to the numbers - 5^150 is roughly 7*10^104 which is still a huge number. As David says, combinatorial arguments like this are a bit of a distraction.


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Mechanism of the calcium-activated protein, Aequorin
In Aequorin, coelenterazine acts as the luciferin, producing light in the presence of calcium and oxygen.
It is unclear to me what part of the protein structure actually catalyses this reaction after the conformational change, and I do not know quite where to begin to find this information.

My edit of your question was to make the title more general, informative and consistent with the actual question, to separate the background from the actual question, and to soften the final remarks. I do not think I have changed your meaning, but do say if I have.

The scientific question
The poster is interested in how the fluorescent protein, aequorin, catalyses the production of light. He mentions the requirement for calcium and oxygen, the role of coelenterazine as a “luciferin”, and is aware of the fact that the protein undergoes an conformational change. He specifically asks

“what part of the protein structure [my emphasis] actually catalyses
this reaction after the conformational change”

I think this is best answered — and will be more useful to those who are not familiar with this protein — by first considering the overall process, and then looking at what is known about changes in structure and how this can be interpreted.
The sequence of event in aequorin fluorescence
Fluorescence of aequorins such as aequorin or obelin occurs through a cycle of events:

The protein (apoprotein) non-covalently binds the organic prosthetic group, coelenterazine, and molecular oxygen
Coelenterazine is ‘activated’ by oxidation to 2-hydroperoxycoelenterazine†
Calcium ions bind to the apoprotein
Activated coelenterazine is converted to coelenteramide and molecular carbon dioxide with concomitant release of blue light
Coelenteramide and calcium ions are released from the protein

I would imagine that coelenteramide would be converted back to coelenterazine by some process, rather than being degraded, but I have not been able to find information on this point.
†In the papers I looked at for this answer I did not encounter information on this, albeit important, aspect of the topic. No doubt such information exists.
The substrate and effector binding sites on the protein
Our knowledge of the molecular details of catalysis by proteins depends on determining structures in which the protein is ‘frozen’ at one particular stage of a reaction. In this case it is not too difficult to crystalize the protein bound to either coelenterazine or to calcium ions, but the reaction and release of these molecules hinders finding a stable structure with both bound. The structures below from the work of Liu et al. show obelin, first with bound coelenterazine, and then with bound calcium ions, although here the coelenterazine has been converted to coelenteramide. This is useful for seeing the relative positions of ions and prosthetic group within the apoprotein.

It can be seen that the three calcium ions (red balls) are bound to similar helix–loop–helix domains called EF hands which are also found in other calcium-binding proteins. In fact, the molecule has pseudo-symmetry with four such domains, but one of them does not bind calcium. The large binding site for coelenterazine is in the centre of the molecule and involves parts of the helices of the EF hands. Because of the cartoon representation, which ignores the side-chains, the binding site appears much more open than is the case.
Conformation changes on binding calcium ions
Let us consider this first from a general standpoint. Because calcium ions bind to the amino acid side-chains of EF-hands through many polar interactions and hydrogen bonds, there is a structural difference between the bound state and the unbound state, where different interactions of these side-chains will occur. Such structural changes at the calcium-binding sites are accompanied by structural changes at distal positions in the protein, including the site at which a substrate binds. This, in turn, can affect the conformation of the substrate, facilitating its reaction.  Although it may be most appealing to consider the effect of the binding of calcium or other effectors as initiating a concerted chain of events, it is perhaps more often regarded as affecting the position of equilibrium between two alternative conformations of a protein, differing only slightly in thermodynamic Gibbs free energy. This latter relates more easily to the comparison of two crystal structures of a protein, where there are “before” and “after” situations to compare.
In the case of obelin, the two structures (above) show anticipated, although relatively modest, structural differences at the calcium binding site. I do not reproduce them here as they are best inspected with a pair of stereo glasses in a printed copy of the paper Liu et al.. The same is true for the changes in the substrate binding site, but it can be seen from the figure above that there is a change in conformation of the substrate after carbon dioxide is released.
The two-dimensional comparison (below) is pertinent as it shows (as does the work of others) that there is a particularly marked change in the interaction of a specific tyrosine and histidine residue (Tyr190 and His175 in obelin, here, and Tyr184 and His169 in aequorin and that of Tyr138 (Tyr132 in aequorin) at the other ‘side’. Changes in bonding to water molecules are also seen (discussed below).

[From Liu et al. (2006) Comparison of the hydrogen-bond network in the binding cavities of obelin before (A) and after (B) discharge of calcium ions.]
How does the conformational change cause bioluminescence?
The mechanism of bioluminescence is outside my sphere of competence, and ideas on how this is triggered in aequorin are based on a range of other experiments. However the following may be of interest:
In 2000 Head et al. wrote, regarding aequorin:

Displacement of the helices flanking the C-terminal loop would be
expected to disrupt the hydrogen bonding of the loop, resulting in
relocation of the side chain of Tyr 184 [Tyr190, above]. This is in
turn would disrupt the hydrogen bonds to His 169 [His 175, above] and
the peroxide. No longer stabilized, the peroxide would be free to
attack the carbonylic C3 to initiate the light-emitting reaction.

Liu et al., writing in 2006, elaborated on this by including a role for the water molecule (W2), the change of position of which they had observed (above).  They proposed the following reaction scheme:

How does a physical scientist go about finding — and understanding — information on proteins?
In my original answer I focussed on how to find information about proteins. That I retain in a more condensed form below. It appears that the poster has a strong background in the chemistry relating to this work, but has had little contact with proteins. As someone whose first degree was in chemistry and then moved into molecular biology, I sympathize. However, although one’s chemistry makes it easy to understand the chemical principles in protein chemistry, one still has to become familiar with the structure of proteins and accustom oneself to what may seem a strange world of weak interactions and non-standard environments. There is no avoiding the need to read at least the chapters on proteins and enzymes in a solid text like Biochemistry by Berg et al., and for this purpose any old second-hand edition will do.
With this background one can, of course, use a general search engine or Google Scholar to search for information on a particular protein. However when these methods fall short I usually go to the Protein Data Bank and search for the protein involved. In this case I used the two terms, aequorin and coelenterazine. This gave me a choice of different structures. I browsed through them, had a look at the 3D views, and then tried to find a relatively recent structure which had a publication associated with it. In this case I chose 7O3U.pdb, which has a related 2022 paper in Protein Science that seemed to discuss the mechanism and active site. From there I worked back to the two papers which are cited in this answer.

Thank you for your response. I am not particularly familiar with protein classification, as my background is more on conventional chemistry rather than biochemistry. Not exactly savvy with the Protein Data Bank. Seems like a massive data load that makes finding the catalytic moiety hard. If anyone else with a better background in this wants to give it a run, feel free.

I have now addressed the scientific question and edited my general advice on finding info about proteins. I would stress that the structure of aequorin is not particularly complex, although the reaction(s) it catalyses and the way it does so are. To go further than this answer you will need to read the original literature, and to do that you will need to have mastered at least the basics of protein chemistry.


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Extra-mitochondrial conversion of Acyl Carnitine to Acyl CoA
Normally fatty acids in the form of acyl CoA are converted to acyl carnitine in a reaction catalysed by carnitine palmitoyltransferase I (CPT1), which is also known as carnitine acyltransferase I. This allows them to be transported across the inner mitochondrial membrane by a translocase when the acyl CoA is regenerated in a reaction that is chemically identical but catalysed by a different enzyme, carnitine palmitoyltransferase II (CPT2).
As a result of observations I have made (detailed below) I wish to known whether acyl carnitine that has not entered into the mitochondria — either present in the cytosol or blood/plasma — can be converted back into acyl CoA without entering mitochondria?
Essentially, does a reaction like that catalysed by CPT2 occur outside of the inner-mitochondrial matrix?
Elaboration
I'm studying plasma metabolites. During fasting there is an increase in plasma acylcarnitines due to increased fat utilization/beta oxidation. If the fast is broken, acylcarnitines are typically supposed to drop. Oddly, some people experience an increase in plasma acylcarnitines 0-30 minutes following eating - but then they drop after the 30 minutes. I'm confused as 30 minutes after food ingestion, elevated circulating insulin levels are still present and should be still working to inhibit the majority of fatty acid oxidation - yet the odd increase and then drop in acylcarnitines after 30 minutes of food intake still exists.
So it leaves me with the question, is there another pathway in which acylcarnitines are converted back to acyl CoA outside of the mitochondria? In short, how does the cell recall fatty acids that are destined for the mitochondria?

This is a rather precise question in a specialized biochemical area, but seems rather strange to me. Is there a reason for asking? If you can explain a little further it is more likely that someone will be able to help you. At the moment all I can do is summarize what I can glean from standard biochemistry texts.

@David I updated the question to reflect your comment. I understand this is a harder question, not a lot research out there on it, but I was hoping to throw this out there to see if anyone has heard anything or can point me in a direction to research further.  Regarding the strangeness of the questions, it is basically introductory metabolism (beta-oxidation) with a twist.

Your clarification was helpful, and after a first go at an answer I have modified your question to provide the background biochemistry for anyone not familiar with it.

The introduction to Ann N Y Acad Sci. (2004) 1033:17–29 lists the various carnitine acyltransferases and mentions CPT-1a, CPT-1b, CPT-1c (tissue specific) but states there is only a single CPT-2 in humans. It does not appear that there is any other variant, so extra-mitochondrial conversion of acyl carnitine to acyl CoA would require a post-translational variant of CPT-2, or CPT-1 working in the reverse direction.
The discussion of carnitine metabolism in Berg et al., Section 22, implies the reaction is near equilibrium. Hence, if the concentrations of substrate and product were appropriate it would be thermodynamically possible for CPT-1 to operate in the reverse direction.
Thermodynamically possible does not necessarily mean enzymically possible. I am not familiar with kinetic studies on CPT-1 and CPT-2, but imagine that CPT-1 has a higher affinity for acyl CoA and carnitine than for the product acyl carnitine, and that the reverse situation holds for CPT-2. I imagine that the ability of CPT-1 (or one particular isoform) to catalyse the reverse reaction in physiological circumstances would depend on its Km for acyl carnitine and the concentration of the latter. It might be worth seeing what kinetic analysis has been done.
The ‘appropriate’ situation for (2) might be if something were preventing utilization of acyl carnitine in the mitochondria of ‘target’ cells.
If you work in this area you will know better than me that there are various clinical conditions and sub-clinical conditions (e.g. obesity) that result in abnormal utilization of acyl carnitine. Could the abnormal instances you observe be for such individuals?

I don't claim that this is a complete answer, but it tries to address the question in terms of possibilities. It has been modified since I originally wrote it.

Awesome, thanks for editing the question, and providing a more than substantial answer. Personally, I was thinking that there could be affinity exchanges, perhaps a short-chain acyl-coa might be a preferred substrate of CPT1, and thus might remove carnitines (somehow) from long-chain fatty acids in favor of switching the carnitine group onto a short-chain acyl-coa. That is just a completely unresearched guess though. I do work in the field of metabolomics, but surprisingly this is an unanswered question. But anyway, thanks again for the informative response.

@Aaron43 — Glad you found my remarks of use. I appreciate the difficulty of interpreting metabolomics data. One problem is that classical biochemical metabolic research went out of fashion because it seemed more or less finished and there were newer and more exciting fields that deserved research funds. However now that the old guys are gone there's a serious shortage of people who understand metabolism to interpret all the new omics stuff. I looked down on it too, but was obliged to teach it in the later stages of my career. Discovered that there are lots of interesting questions left.

lol, the complexity and the almost infinite number of metabolic interpretations that can come from something as simple as plasma metabolite concentrations, really makes the field seem like chaos. Even my own work I have to step back sometimes and just say wtf. Ha, but thanks again for the info.


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1mm-long insect ID from Tennessee
I live in east Tennessee. I went outside today (May 27.2017) and saw all these tiny insects all over my truck.
They are yellowish in color and have 6 legs, one solid body (including head). They move pretty quickly (like a chigger)
What are they?

East TN you said. Does TN stands for Tenessee or Tunisia (both being typically abbreviated TN)?

Very important to mention that they are six-legged.

@adjan and I are being a bit mocking today! Sorry about that. I edited the post assuming that you live in Tunisia (given your user name and given that a Tunisian would probably name the country fully by fear people would not understand). I  also removed the (quasi-) tautology (6-legged insect). +1

@Remi.b "I edited the post assuming that you live in Tunisia." "I live in east Tennessee." ;)

That was a typo.

Welcome to SE Biology. I know that computer graphics are difficult, but the photos you have posted do not display in my browser because they are about 10 times larger than necessary and do not show enough detail. I have processed the first for you, but if you need to post again, do an internet search to find out how to downsize photos.

The only reason I uploaded the large photos is so that you could zoom in and see the insects better, (The better to see you with my dear ((Wolf))

Thanks for all the comments, yes, east tennessee

I thought it might have been a Thrip, wasnt sure about that

The insects you have found must be of a species of thrips. This excerpt from Wikipedia fits your description well:

Thrips (order Thysanoptera) are minute (1 mm long or less), slender insects with fringed wings and unique asymmetrical mouthparts. Different thrips species feed, mostly on plants although a few are predators, by puncturing and sucking up the contents. Approximately 6,000 species have been described.

I won't try to identify the exact species, but here is a photo of a yellowish-orange thrip I have found:

Image source:
https://6legs2many.files.wordpress.com/2012/04/thysanoptera_thrips_fringe_wings.jpg


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Thermodynamics of passive transport
My question is, where does energy come from for passive translocase's conformational changes? I argue it can't be concentration gradient, as concentration is only statistical phenomenon at micro scale, and has nothing to do with energy of individual molecules and interactions. I also don't want to cover electric gradient, as it involves obvious electric forces.
I couldn't find any diagrams like this about this theme, so I would appreciate very much if someone provides me with one:

I am not sure that the concentration gradient provides the energy for conformation changes in passive protein transporters (or at least the molecular mechanism), but your statement about a concentration gradient being unable to energy is obviously incorrect or Mitchell's hypothesis would have been thrown out years ago. Instead it won a Nobel Prize. (And that involves an electric gradient as well, whether or not you want to cover it.)

@David thank you for your response. concentration of molecules doesn't correlate to energy of each particle, but temperature does. i did not want to cover electric forces as they are already obvious, moreover, not all particles have charge, e.g. glucose.

I said concentration gradient, not concentration. There is a page in Berg et al. that derives the thermodynamic expression for the free energy change represented by a concentration gradient. Unfortunately this is no longer available online.

Type of transport to be considered
The term used in the question — passive translocase — is not a standard description of any transporter protein. From the description I shall assume we are talking about what is called Passive Transport or Facilitated Diffusion. This is defined in the Wikipedia article on the topic as follows:

Facilitated Diffusion… is the process of spontaneous passive transport (as opposed to active transport) of molecules or ions across a biological membrane via specific transmembrane integral proteins. Being passive, facilitated transport does not directly require chemical energy from ATP hydrolysis in the transport step itself; rather, molecules and ions move down their concentration gradient reflecting its diffusive nature.

Although most structural information is available for ion transport, because of the specification of the question, I shall consider the transport of glucose (and other neutral sugars) by the proteins GLUT1 and GLUT3
The molecular concentration gradient supplies the energy for transport
Before considering the molecular interactions between the sugar and the transporter protein, it is necessary (because of the assertion otherwise in the question) to assert that the net difference in concentration of sugar between the two sides of the membrane supplies the overall energy for transport.
The free energy change in transporting a neutral species from one side of a membrane at a concentration c1 to the other side at a concentration c2 is:

ΔG = RTln(c2/c1) = 2.303RTlog10(c2/c1)

For example, if c1 = 10–1 M and c2 = 10–3 M, one can calculate the change in Free Energy as –11.3 kJ/mol.
General aspects of the thermodynamics of conformation changes in proteins
Many protein, e.g. allosteric proteins such as haemoglobin, can adopt two (or more) conformations differing only slightly in Gibbs Free Energy. Clearly, the conformation with the lower free energy will be favoured. However the position of the equilibrium between the two states can be changed by the specific binding of a small molecule which can favour the disfavoured structure, because the protein–ligand complex has a different, and lower, free energy than that of the free protein.

A general alternating model of transporters was proposed by Jardetzky as long ago as 1966, assuming three characteristic features:

A cavity in the transporter to accommodate the substrate
Two different transporter conformations to allow for the molecular cavity to be open to one side of the membrane in one conformation and to the opposite side in the other
A binding site for substrates in the cavity, the substrate affinity of which may be different in the two conformations.

Detailed thermodynamics of the GLUT transporters
Zhang and Han (Biophysics Reports 2016) performed the kind of thermodynamic analysis solicited in the question in the light of structural information on GLUT transporters of the major facilitator superfamily (MFS). They considered two conformation states — Cin and Cout, with and without bound substrate in a four step model:

They also presented a free-energy landscape of the type requested, concluding that the lower free energy of Cout after transport was due to loss of energy as heat.

For a full explanation it is, of course, necessary to consult the original paper.

Thank you very much for your expertize. I wonder weather  lower free energy of Cout after transport increases after regaining thermal energy from surroundings. That should finally answer my question.

@nikopapiashvili — I'm not an expert on transporters, and I do find this a bit puzzling myself. I would need to read and think a bit more about this. There are some protein chemists on the list that are more knowledgeable than me on thermodynamics. Perhaps they will chip in.


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Has any research lab done serious work to engineer new bacteria which assemble graphene wafers?
I was thinking about crazy uses for engineered bacteria. Nano-assembly of Graphene seems like a potentially excellent target for the technology. Have any research/full-blown labs worked on this? Any papers on it?
What would be some of the difficulties?

Surprisingly, the answer is yes. In 2012 Tanizawa et al published a paper titled Microorganism mediated synthesis of reduced graphene oxide films. The gist of it is that most of the steps (including the structuring of the graphene sheet) were carried out with chemical synthesis, but a final reduction step from graphene oxide to graphene was carried out using bacteria from a local river.
Probably not quite what you were thinking of, but I imagine this is the closest you'll get for right now.

cool... as I am interested in nanotech, this is very impressive...+1


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Sweating at all temperatures
Is sweating possible if surrounding temperature is below the body temperature? How the sweating occur due to the combustion of food?

Most people most of the time live in the environments that have lower temperatures than it is their normal body temperature (36-37 °C). And most people sweat sometimes at these temperatures.
In the summer, when it is 30 °C and you wear only swimming trunks, even light walking can make you sweat. The same can occur in the winter when the ambiental temperature drops below 0 °C and you wear warm clothes. This is because the muscles, when working, can generate more heat than you need and sweating is the way to get rid some of it.
When you eat food and the food is broken down to release energy, some of this energy will be released as heat. If the food generates more heat than your body needs, eating foods, especially ones high in protein, can make you sweat.
Some people get sweaty after eating certain spicy foods. This is called gustatory sweating, which is not related to food combustion, but it is a neurological phenomenon.
Capsaicin in red hot chili peppers can also trigger heat generation and sweating.
Drinking alcohol dilates the blood vessels in your skin, which results in increased flow of warm blood through your skin, which can signal the thermoreceptors in your skin to trigger sweating.

Indeed, I've been known to work up a good sweat while cross-country skiing in nothing but light pants and a T-shirt.


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Why do the phosphatidylserine and Phosphatidylethanolamine favor one side of the cell membrane?
Thie picture below shows that the phospholipids phosphatidylserine (PS) and Phosphatidylethanolamine (PE) are more likely to be found on the inside of cell membranes than on their exterior.

Why is this so? What prevents them from creating a shape that is wave-like (illustrated) or some other shape?

Welcome to SE Biology. I have edited your question slightly, especially to define abbreviations. Please finish reading the [Tour] as it will help you understand how this site operates.

I’m not sure if this would help answer your question, but in living organisms the lipid composition of each membrane leaflet is highly regulated. A flippase translocates PS and PE to the cytoplasmic side of the membrane.

There seem to be two questions here.
The poster seem to know the answer to the first question — that in the title — that their shape fits into one or other side of a curved membrane. So I would recommend the title be edited to address what appears to be the main concern.
Instead of “Why do these phospholipids insert into one side of an already spheroidal cell membrane?” the concern appears to be the effect of the insertion on the shape of the membrane: “Why doesn’t the insertion of these phospholipids cause a wave (ruffled rug) shape, rather than a spheroid?”
If this is, indeed, the question then the answer would be that the ‘empty spheroidal’ shape of cell membranes is determined by other forces, principally thermodynamics. The main one is that which causes a lipid bilayer in the first place — the polar head being oriented to the aqueous environment, whereas the hydrophobic tails are in contact with one another. This still leaves hydrophobic “edges” to any membrane sheet, which therefore fuse into a hollow spheroid to remove them from contact with water.
So, although I am not a cell biologist, I would hazard that the wedge-shaped phospholipids help relieve bending stresses in a membrane that has already adopted a spheroidal shape for thermodynamic reasons.


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Why do bacteria need the CRISPR system?
I'm learning about CRISPR at my college. I understand that when viral DNA is inserted into a bacterial cell, the Cas1-Cas2 proteins identify the PAM site in the viral DNA and then cut the protospacer from the viral DNA to make it a spacer in the CRISPR array for the adaptive immunity of the bacteria.
I'm confused about why a complex CRISPR system is necessary if the Cas1-Cas2 cuts the protospacer, and at that time only the viral DNA gets inactivated.

What do you mean by "a complex CRISPR system"? Every part of what you've noted makes sense to me except the question. Can you draw a picture of the system, point out what you understand, and what doesn't seem necessary? (Or more likely show some course materials)

My motive was to ask if the Cas1-Cas2 protein can cut the viral DNA by identifying the PAM site, and then the viral DNA gets inactivated. Then why do we need Cas9 then?

I'd suggest reading the Cas9 wikipedia page. If that doesn't make sense, you can come back and edit your question to indicate what you find confusing. (Ordinarily we ask posters to do some background research of this type as part of asking their question- see here about our homework policy and see here for a tour of the site to learn more.)


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Why don’t animal cells fall apart when they are out of water?
Cell membranes are formed because of the phospholipid's shape and properties. The hydrophilic heads will arrange themselves to surround the hydrophobic tails, so the hydrophilic heads always face the water while hydrophobic tails are shielded. But out of water, there is only water on the inside, and not outside, so shouldn’t the cell membrane just fall apart when the cell is out of water?

But do animals really dry out without dying? I mean...early land animals like amphibians die if their skin dries out and more developed land animals have mechanisms to protect from drying out while the insides of animals are universally wet.

Why would a cell membrane fall apart when out of water? interaction forces between neighboring phospholipids don't disappear.


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How can one store non-sterile culture media in dissolved form in the refrigerator?
How do I store non-sterile culture media in dissolved form in the fridge in a clean but non-sterile container?
The powder of the media (Broth, Nutrient agar, MAC, or MH agar) will be put in a glass bottle filled with distilled water and then dissolved/mixed in the microwave.
Would a 12-hour to 16-hour storage in the fridge prior to sterilization, thereafter, affect the media performance?

So long as you are careful in making this, so as to not add gross+ contamination (hair, don't put your fingers in it, etc.) and use clean glassware, then a storage at 4 C will inhibit almost all bacterial growth from almost all common species, and those that are capable of growing at 4 C tend to grow very slowly.
You don't need to microwave before sterilization generally - the autoclave will melt the agar much better than you can do in the microwave and is easily mixed in by a swirl of the bottle after removing from the autoclave.
+ This means bulky or heavily, not "ewww disgusting". See definition 4: https://www.merriam-webster.com/dictionary/gross

I'm melting to mix. Do you mean that i generally don't need to mix prior to autoclave, just add powder + water, then autoclave and swirl after its out?

@FreezingSoul you should dissolve liquid media in cold water, then autoclave. Media with agar, you should dissolve the soluble components in cold water add the agar (if separate), then autoclave. No need for microwave to dissolve the agar.

I meant to ask, generally, is there no need to mix prior to autoclaving? I think i had pimpled MacConkey agar when i didn't boil it prior to autoclaving.

I didn't swirl, to be honest after receiving my autoclaved media, but it was clear.

@FreezingSoul I usually keep a magnetic stir bar in the flask when autoclaving media. Makes it easy to mix while cooling, which is especially important when I have to add heat-sensitive amendments (like vitamins or certain amino acids). I honestly wonder why every SOP ever tells us to dissolve agar with heat before autoclaving, since every lab person I know just mixes it in cold and lets the autoclave do the heating/dissolving.

Media performance in terms of what? What are the temperatures in the fridge?
Assuming you are storing sterile media, refrigeration will not affect anything. What might be affected is the media and culture. Your question sounds like you are storing media without cells, and nothing will be affected.

"Non sterile", not "sterile"


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Postulate that one sex will put more resources into reproduction than the other
What is the name of the idea that because one sex will put more resources into reproduction than the other, that sex will try to minimize the number of mates (choosing the best one) and the other sex will try to maximize the number of mates?

Welcome to SE Biology. Please finish the [Tour] to learn about this site. I have taken the “law” into my own hands, as the term is alien to Biology. Let’s leave it for the physical and mathematical sciences.

I don't know if a named "law", and even where those exist it's a bit misleading to use that term because the things called laws in biology (which describe things that often have many exceptions) are nothing like laws in physics (where finding exceptions would be treated as rewriting our basic knowledge of physics).
Anisogamy means differently sized gametes. That Wikipedia page mentions some papers that discuss reasons that one would expect a tendency (but not guarantee) to evolve anisogamy:

Geoff Parker, Robin Baker, and Vic Smith were the first to provide a mathematical model for the evolution of anisogamy that was consistent with modern evolutionary theory.[4] Their theory was widely accepted but there are alternative hypotheses about the evolution of anisogamy.[9][1]

(1) Lehtonen, J.; Kokko, Hanna; Parker, Geoff A. (October 2016). "What do isogamous organisms teach us about sex and the two sexes?". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 371 (1706). doi:10.1098/rstb.2015.0532. PMC 5031617. PMID 27619696.
(4) Lehtonen, Jussi (2021-03-05). "The Legacy of Parker, Baker and Smith 1972: Gamete Competition, the Evolution of Anisogamy, and Model Robustness". Cells. 10 (3): 573. doi:10.3390/cells10030573. ISSN 2073-4409. PMC 7998237. PMID 33807911.
(9) Majerus, M. E. N. (2003). Sex Wars: Genes, Bacteria, and Biased Sex Ratios. Princeton University Press. pp. 7–8. ISBN 978-0-691-00981-0.

You are probably thinking of Bateman's principle.
It states that since males are capable of producing millions of gametes that are much "cheaper" than female gametes, males maximize their reproductive success by increasing the number of females they mate with. On the other hand, females are limited by the number of eggs they produce.
Following this, the result would be sexual selection, where males compete for the access to females whereas females are more choosy. By doing so, females might maximize the quality of the male they mate with, and potentially the success of their offspring.

Can you please not just drop a link but actually explain something in your answer? This is more a comment.

I'd describe Bateman's principle as explaining why anisogamy should be expected to produce certain characteristics like increases variance among individuals of the smaller gamete sex, rather than explaining why anisogamy exists at all.

But this was not the question though. The person asking was thinking of Bateman's principle. I elaborated instead of providing a simple link.


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Examples of environmentally influenced gene-expression in humans?
In discussions of the relevant importance of genetic and environmental influences on the development of the individual, it's often stated that the genetic and environmental influences interact.
An example that is often given is a certain kind of rabbit (usually white), carrying a particular gene for fur color. When the proper allele is present, AND the rabbit is exposed to cold, it will a dark spot on its fur. When the allele is present, the dark spot does not develop without the cold, and when the rabbit has the opposite allele, the spot will not develop even with cold exposure.
This is fine, but when I want to explain genes and environment to people, it has two pedagogical flaws:
(1) it's about rabbits
(2) it's about a trait people don't really care about
Is there a human example of this phenomenon?
That is, a phenotype which requires BOTH a certain genetic background and particular environmental influences in order to be expressed?

Not answering your question but if you want to read a small introduction in the theory describing how the environment, genetics and other things affect phenotype, you should definitely give a read to this post

The rabbit example seems to have at least three pedagogical benefits: (1) it's a simple Mendelian gene (I presume), (2) it's easily and ethically inducible (cold exposure), (3) it's a visible and obvious example of a phenotype: fur color. There are many many human gene-environment interactions but most are studied in the context of disease and are far more complex.

Could you please give an example? Relevance to human health is exactly what I am looking for.

@Maringo7 There are so many examples of health related traits that have a non-zero (and non-one) heritability in humans (lung, breast and ovarian cancer, schizophrenia, depression, back pain, sensitivity to common cold, ...) but I can't think of anyone that particularly stand up as a classical example for kids.

Would carcinogen exposure (an environmental influence) and cancer be a good example for you?

What about skin pigmentation? It is influenced by genes and by the exposure to UV. http://www.jbc.org/content/282/38/27557.full.html and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093193/ may be a good place to start.

How about entire sections of the X chromosome in males, various active parts of the immune system, or everything involved in pregnancy.

The breadth of examples of environmental exposure directly influencing changes in gene expression in humans is astonishing, occurring at every developmental stage from conception  to death.
As an example, consider the environmental exposure to a reasonably high dose of a gram negative bacteria with lipopolysaccharide. Immune cells recognize this very particular environmental exposure as a danger signal, triggering a signaling cascade that includes activation of nuclear factor kappa beta, or NFKB.  A series of changes in gene expression begins, including transcription, translation, and release of interleukin-1 and TNF-alpha, which are responsible for a host of externally observable changes, not the least of which is an increase in your body temperature.  You can read about this generally in any introductory clinical microbiology or immunology text. One example is Murray Medical Microbiology, Ch. 2.
In this example, exposure to an infectious agent is analogous to cold weather in the rabbit. Fever is analogous to the change in the rabbit's fur color.
As acvill’s answer indicates, the color change in rabbits is not mediated by gene expression. In the case of fever, though, it is, and may be a useful teaching example. Everyone has experience with fever and understands that fever is not the basal state, but a response to the environment. It is not hard to make the leap from that personal experience to the idea that the signaling molecules that cause fever are not typically present, but are in response to very particular environmental cues, and that change (from the absence of circulating IL-1 and TNF-alpha to the presence of IL-1 and TNF-alpha) is controlled by a famous and fun to say transcription factor, NF-kappa beta.

I think your question is interesting, though the use of "expression" is misleading in context of your rabbit example.

Examples of environmentally influenced gene-expression in humans?
...
That is, a phenotype which requires BOTH a certain genetic background and particular environmental influences in order to be expressed?

In the example you give, the color-changing phenotype is not due to changes in gene expression but rather a conformational change in a tyrosinase variant at low temperatures that leads to decoupling of an inhibitor from the enzyme.  This is not to say that there aren't any changes in expression with changes in temperature -- only that the phenomenon you describe is ultimately a change in enzyme activity and not the induction of a specific allele.  See Kidson and Fabian, 1981 [1] --

It is proposed that at the normal body temperature of 37 degree C, tyrosinase from Himalayan skin is strongly bound to an inhibitor. At lower body temperatures, the affinity of the enzyme for the inhibitor decreases, thus allowing the synthesis of melanin to increase. This change in affinity of the enzyme for the inhibitor could be regulated by temperature-induced conformational changes in either the enzyme or the inhibitor or both.

Note that this study was conducted in "Himalayan" mice, not rabbits, though the authors do reference an earlier rabbit study [2] --

These results are in support of Danneel's visual observations ('41) that "ferment" activity of Himalayan rabbit skin is absent at temperatures above 25 degree C.

the full text of which can be found, in German, on Google Books.

Concerning a human example of allele-environment interactions, look no further! The same temperature-sensitive tyrosinase mutation has been reported in people with oculocutaneous albinism (OCA) [3], albeit with a slightly different phenotype.  From the abstract:

In this paper, we report a new type of OCA that results from a tyrosinase allele producing a temperature-sensitive enzyme. The proband had white hair in the warmer areas (scalp and axilla) and progressively darker hair in the cooler areas (extremities) of her body. Melanocyte and melanosome architecture were normal. Quantitative hairbulb tyrosinase (dopa oxidase) assay demonstrated a loss of activity above 35-37 degrees C. Plasma pheomelanin and urine eumelanin intermediates were reduced and correlated with hair melanin content. This is the first temperature-sensitive tyrosinase mutation to be reported in humans and is analogous to the Siamese mutation in the cat and the Himalayan mutation in the mouse.

References

Kidson SH, Fabian BC. The effect of temperature on tyrosinase activity in Himalayan mouse skin. J Exp Zool. 1981 Jan;215(1):91-7.
Frisch KV, Goldschmidt R, Ruhland W, Winterstein H. Ergebnisse der Biologie. Eighteenth Volume.
King RA, Townsend D, Oetting W, et al. Temperature-sensitive tyrosinase associated with peripheral pigmentation in oculocutaneous albinism. J Clin Invest. 1991;87(3):1046-1053.

This answer is almost too perfect.

I did not read this carefully enough on the first pass... agreed! Good frame challenge.


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Sex identification of two white checkered Skipper butterflies
I have two white checkered skippers and ik for a fact one is a female(at least i think) but im not sure abt the other one? Can some one tell which is which or if there the same sex? One butterfly has a bulkier body with larger wings and wingspan with a smaller head which I believe that one's a female the other one has a smaller body smaller Wings in a bigger head which I believe to be a male but I'm not sure can somebody help me sorry about the picture quality my phone takes bad pictures

It’s “sex”, not “gender”, and we use standard English, not textese on this site, the details of which you are expected to read about by finishing the [Tour].

Any sex determination here would be speculation.
Butterflies and Moths of North America has this to say about Burnsius albezens. Note the bolded last sentence:

Identification: Paler than Pyrgus communis. Male often has complete black checks in wing fringes. Upperside of male is blue-gray; female is black. Both sexes have large white spots which form median bands across both wings. Male has a costal fold enclosing scent scales on the upperside of the forewing. Underside is dull white with dark gray bands. Positive identification can be made only by dissection and scrutiny of the male genitalia.


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Which predators only eat some parts of their prey? (Warning — graphic content)

In an small city in middle-east somewhere near a desert, an unknown predator attacks sheeps, goats and chickens. These attacks began a few weeks ago and until now more than 150 sheeps have been attacked. It causes panic and rumors among people and despite official investigations no result has been achieved yet.

Welcome to Biology.SE. Is there a freely available report for these official investigations?

Where in Middle-East do you live? There are different biogeographical regions in the Middle-East.

I remember a show in which (maybe) this case had been investigated (near Mexico probably) and one scientist there showed a dead chupacabra (or what its called) stored in a glass container!

Any predator that cannot eat the entire animal at once.

Scavenger birds also leave carcasses like that since they can't break up the bones and only eat the soft tissue. This produces a hollowed out carcass like that. Although birds will usually eat the tongue and eyes as well.