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Are all mutagens carcinogens?
Not all carcinogens are mutagens. Alcohol and estrogen, for example, does not damage DNA.
It's one of the assumptions of the Ames test that mutagenicity implies carcinogenicity, but is this always the case? I assumed that it was, but then I saw one of the comments here. I did some more research but the internet seems to be reluctant to be definitive on the subject. This guy claims 'no', but I'd prefer sources or at least a response that handles counterexamples like HPV. This paper claims 'yes', but doesn't list any specific examples. Some mutagens might be more specific to genes involved in cell cycle regulation, so I could see how a weak mutagen is a powerful carcinogen.
My question is, can you go the other way? Are there mutagens that just do not cause cancer? If they do not exist or are not known to exist, are they even possible?

Short answer
All mutagens are potential carcinogens unless the mutagen is highly specific to a site. As noted in the question, carcinogens need not be mutagenic.

HPV causes oncogenic transformation of a cell because of certain proteins that it expresses. HPV is considered a carcinogen by the IARC. Some retroviruses are oncogenic: they might carry an oncogene or insert randomly near an endogenous proto-oncogene and cause oncogenic transformation; this phenomenon is called insertional mutagenesis (Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses). They can also integrate within a gene and knock it out. Many of these viruses are considered carcinogens by IARC.
Hepatitis viruses (B & C) can also induce carcinogenesis but insertional mutagenesis is not the sole mechanism (Cougot et al., 2005; Fung et al., 2009; Lemon & McGivern, 2012). Hepatitis viruses are considered carcinogens by IARC.
Ethanol in alcoholic beverages is considered carcinogenic by IARC. There are many substances listed as carcinogens by IARC but they are not mutagenic. The general mechanism of carcinogenesis by these substances may be prolonged inflammation or ROS generation.
Loss of function of the tumour suppressor gene p53 leads to cancerous progression (Chiche et al., 2016; Venkatachalam et al. ISBN:978-1-59259-100-8). So an siRNA that targets p53 should be called a carcinogen. It would however not cause any mutations and is hence not a mutagen.
If you consider the tools developed for genome editing, such as ZFN, CRISPR-Cas and TALEN as mutagens then they are not carcinogenic. However the term mutagen is not used for these molecules. Mutagen almost always refers to a molecule that causes random mutagenesis thereby making it a potential carcinogen.

I'm no expert on the matter, but just quoting from Wikipedia:

Mutagens are not necessarily carcinogens, and vice versa. Sodium Azide for example may be mutagenic (and highly toxic), but it has not been shown to be carcinogenic.

It cites Toxicology And Carcinogenesis Studies Of Sodium Azide.
So it would appear the answer is no. Not all mutagens are carcinogens.

Sodium azide is only mutagenic part of the time(half of the strains tested), and there's http://www.ncbi.nlm.nih.gov/pubmed/2671718 this paper that shows that sodium azide isn't a mutagen in mammals. It's still poisonous (cerebral necrosis!) but neither a mutagen nor a carcinogen in mammals.

It seems like there should be a counter-example (a mutagen with zero or negligible carcinogenicity) but I can't find one.


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Why aren't animals diverse in phenotype?
I am not comparing a cat with leopard.
I am just saying that we humans are all one type of creature and we are diverse (I am not saying we are class of mammals and phylum of etc and kingdom etc, because my religion doesn't believe in it).
So consider the class of cats they are one type of species so why aren't they diverse in phenotype like us?
Why do other animals, plants, unicellular organisms not have diversity in their phenotype and how they can recognize each other, like a bird always brings food to his offspring and it can't make mistake by giving it to other offspring of its own species?
So can I say they aren't diverse because of in their meiosis division their chromosomes don't cross over and random assort (alignment)?

Wait cats and dogs aren't diverse? Look at a Chihuahua and a Great Dane. How much more diversity do you want?

Quick note re. face recognition: human face diversity is similar to other species. It seems greater because we have specific sensitivity to tiny details in human faces (as do sheep to sheep faces, etc). Some people lose this through brain damage or from birth (Prosopagnosia), and without it, human faces are as alike as, say, sheep. Try drawing recognisable likenesses of people and you'll see how tiny our facial differences are: caricature artists exaggerate these tiny details massively to make their drawings reliably recognisable.

(sheep make a good analogy because farmers can (with difficulty) learn to recognise some sheep by their faces like how prosopagnostic people can (with difficulty) learn to tell between some faces by focusing on specific details, and there are studies showing that sheep learn to recognise sheep faces with similar speed, ease and duration to humans learning human faces)

In your question, your assumption that animal species are less diverse phenotypically than humans is wrong. I am sure you will appreciate @terdon's answer to this post and @rg255 answer to this post.
Don't forget that we are good at detecting differences among humans (because we evolved for this purpose). We are doing much worse at telling apart animals from other species just because we have not evolved for this purpose. This is the reason why we tend to see human faces when looking at clouds but we rarely see sheep faces! Several studies (here and here) showed that sheep are able to recognize each other (and we even know the number of neurones needed to remember one face). They are probably better at telling two sheep apart than telling two human apart.
Another interesting fact is the so-called cross-race effect. We, humans, are better at recognizing faces of people from our own ethnic group than faces of people from other ethnic groups. For example, a Japanese is very good at Japanese faces recognition but not good at recognizing European faces. Same is true the other way around.
As @user568459 said in the comments: some people are not able to recognize faces. This is due to a cognitive disease called Prosopagnosia (also called face blindness). Those suffering from this disease are not better at recognizing sheep faces than human faces.

So consider the class of cats they are one type of species so why aren't they diverse in phenotype like us?

There is no good definition I think of what is phenotypic diversity (no accurate and objective index to measure it) but at first sight I would tend to think that cats are more diverse than humans. One of the main features one would probably raise when talking about human diversity is skin color. And in terms of color, cats are much more diverse than humans. You may think of an extraordinary diversity when thinking of Norwegian that are taller than Indonesian (I may not have chosen the two extremes) by several centimeters on average but think about cats! The average cat weight 4 to 5 kg but some cats weight less than 2 kg and some other (like the coon cat) weight more than 10 kg (World Record: 21.3 kg). Imagine a human ethnic group that would on average weight 5 times more than another ethnic group! And think also about cats' hair length or tail shape! Humans vary in terms of facial feature (lips size, nose shape, etc.) so do cats. Some look like their face was smashed against a wall while others have a long muffle. Again I welcome you to have a look to this post.

how they can know each like a bird always brings food to his offspring and it can't make mistake by giving it to other offspring of it's own species?

As I said above humans evolved to recognize their own. Many species also evolved in order to recognize their own. In some species individuals use smell rather than visual features in order to recognize each other (odor is also a kind of phenotypic variation). But still some species are poor to recognize each other. For a bird, it seems rather easy to not feed the wrong individual as all their offspring are usually together in the same nest. However you might be interested the lifestyle of the cuckoo who parasites nests of other bird species. Cuckoos' babies and particularly the inner beak resemble to the babies of the species they parasite and often the parents (often the mother only is involved in feeding the young) get fooled and feed the cuckoo.

So can i say they aren't diverse because of in their meiosis division their chromosomes don't cross over and random assort (alignment)?

No, you can't say that! Because they are diverse and because for many of the species you may think about, cross-over does occur. Their genetic diversity as well as their phenotypic diversity is as high than in humans. There is nothing extraordinary about humans (except their brain and the related fact that we predigest our food by cooking it) compare to other lineages. And there is nothing extraordinary to have one extraordinary feature (such as a big brain) that you can't find in other lineages! Many lineages are extraordinary in some sense.

I'd like to add that the variations in individuals within a species are a fundamental observation upon which modern biology is standing.  Darwin wrote at least 2 chapters of Origin of Species demonstrating how animals and plants have a lot of individual variations:

Darwin's argument involved four steps.  First, he noted the wide variation between many types of living organisms: between species of plant, fish, bird and mammal; and also between different family groups within the same species; and also between different exemplars within the same family. Wherever we look - and during his five-year voyage on The Beagle in his early twenties, there were few places on earth where Darwin had not looked - we see differences between organisms: different sizes, different colours, different features, different behaviours and, of course, different survival rates. The theory of natural selection takes variation of species and within species as its starting point.

Before that era (he was not the only one who made this argument) pretty much everyone believed that all animals of a given species were the same.
It took quite a while before everyone was convinced, but an entire generation of scientists was won over.
If you need a modern confirmation of this, look into cattle breeding. Individual phenotypes make some bulls worth many thousands of dollars/euros.  Others nothing. Lastly, now that we understand that the basis of inheritance is in the DNA, we can quantitate the specific mutation rates in various genes and segments of DNA and show that they are comparable from species to species.  These vary somewhat, but humans are not exceptional.

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Essential amino acid codons
Essential amino acids also have codons.Still they are needed by humans through diet?Will those codons do synthesize amino acids for some other purposes in humans or not?If so, what is the purpose?e.g?

Codons are like 'put green ink here'. The amino acids themselves are like green ink. Humans can write things in green ink, we just need to go and get some first, because we cannot make the ink. Does that make sense?

You are mixing things. First: Codons have nothing to do with the synthesis of amino acids.
A codon is the sequence of nucleotides on the DNA (or RNA) which code for a certain amino acid. For example UGU and UGC code for the amino acid Cysteine and given these codons it will appear in the protein being synthesized. The codons are basically a way to code the sequence of a protein with the smallest amount of information (simply by the sequence of the four nucleotides in DNA/RNA). For further information have a look at the Wikipedia page on Codons.
This look like this (image from the Wikipedia):

Okay thanks.My question is codons also code for essential amino acids right?Could you please give me an example of an enzyme or any other protein produced by DNA sequence(mRNA--triplet codons--essential amino acid) with essential amino acids in it?

They are the code for this amino acid on DNA/RNA, not more. Their synthesis is done by special enzymes (which are not all present in human, hence we have some essential amino acids) and "only" needs the right precursors.

Try http://www.uniprot.org/uniprot/P02452 for the sequence of Collagen I alpha precursor. Scroll down(pretty far) for amino acid sequence. K stands for lysine, an essential amino acid.

Answer to the comment

Could you please give me an example of an enzyme or any other protein produced by DNA sequence(mRNA--triplet codons--essential amino acid) with essential amino acids in it?

Partial Amino acid sequence of alpha amylase in Homo sapiens:
MKLFWLLFTIGF

Nucleotide sequence:
ATG AAG CTC TTT TGG TTG CTT TTC ACC ATT GGG TTC

Below s the amino acid single letter representation table that can be referred to understand the amino acid sequence

Make sure you follow the reading frame scheme to read the nucleotide sequence. Each time frame should have a triplet codon without including the previous nucleotide. I've represented it for the first few codons. You can observe essential amino acids in this protein. All the amino acids in this partial sequence are essential except glycine. Hope this helps :)

Can you shorten the example sequences? Just show something like 10 codons/aa. It just occupies more space and does not add to more information.

Perhaps worth adding that since most (all?) human initiation codons are AUG, most (all?) proteins contain an essential amino acid right there.

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First RNA polymerase-mRNA
We know that RNA polymerase produces mRNA by reading DNA strand. Which enzyme produces the first RNA polymerase if other RNA polymerases are synthesized in the same way like other enzymes(proteins) ?

Fantastic question :D I look forward to an answer! I've thought about this a lot myself, shame I never found an answer...

it is a chicken-egg sort of question. You can have a look at self replicating ribozymes.

Contemporary cells have RNA pols from the start. If you're asking how RNA pols might have come to be, look no further than RNA-directed RNA pols.

@5heikki Would be great if you could elaborate and put it up as an answer.

not an expert, but i can hypothesize that the sperm or/and the ovule already have some RNA polymerase, and all cells keep somewhat stable this, if you mean how it happened the first time in evolution I dunno. btw cool question

@The Last Wort. I agree. Are the maternal like the mitochondriae, cp. Katz's comment.

The RNA world hypothesis states that self-replicating RNA (that is, an autocatalytic RNA polymerase) was the first form or precursor of life. So, in that context, your question is basically asking how life originated. The obvious answer is that we don't know (currently anyways), but I'm going to take this opportunity to describe a few really neat experiments which might give you some insight over a possibly contributing mechanism of how self-replicating molecules may have developed. I won't go over the Miller-Urey or Oró experiments, but let's assume that the early Earth contained organic molecules (especially nucleotides for our purposes). It's also important to keep in mind the immense time scales over which these processes occurred (the Earth is ~4.5 billion years old).
Anyways, let's talk about in vitro evolution, also known as systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a procedure whereby an initial library of random RNA sequences (flanked by known sequences to be used as primer sites) undergoes a selective process followed by amplification and mutation of the selected molecules. This is repeated several times. As an example, this process can be used to create aptamers, which are small RNA molecules which bind a specific ligand. A pool of random RNA is passed over a column containing the immobilized ligand. By chance, some RNA will have some amount of affinity to the ligand. Poorly bound RNA is washed off non-stringently and then slightly better bound RNA is eluted. This RNA is reverse transcribed and amplified by PCR. The PCR primers contain the T7 RNAP promoter which allows transcription of the cDNA to produce a new  RNA pool. Somewhere in this regeneration process, mutations are introduced so that the new pool contains randomly modified copies of the RNA which had some affinity. Through repeated steps of increasing stringency, an aptamer with high affinity can be developed.

(Ellington, 1994); Outline of the SELEX process.

So how does this apply to the origin of the first RNA polymerase? It just so happens that Bartel and Szostak (1993) used in vitro selection to produce a ribozyme (a catalytic RNA molecule). This ribozyme was a ligase, that is it catalyzed the formation of a phosphodiester bond between two RNA molecules that are aligned on a template.

(Bartel and Szostak, 1993); Methodology of the selection used to generate a ribozyme ligase.

While the ribozyme created was not autocatalytic, the experiment had implications on the origin of self-replicating RNA and life in general, which were discussed in the paper:

The ribozymes that we have isolated from a pool of random sequences catalyze a chemical transformation similar to that catalyzed by polymerases. Their abundance in the random-sequence pool is therefore relevant to the hypothesis that life began with an RNA replicase that originated from prebiotically synthesized random-sequence RNA. We detected about 65 sequences (Fig. 8, pools 3 and 4) capable of carrying out a particular ligation reaction in a pool of more than $10^{15}$ initial sequences, or a frequency of occurrence of one in about $2*10^{13}$ sequences.
[...]
Presumably, sequences capable of acting as efficient template-directed RNA polymerases are more rare than this, and sequences capable of acting as an RNA replicase are even more rare. Evidently, catalysts of moderate activity could arise spontaneously from relatively small quantities of RNA (and perhaps related polynucleotides); however, a catalyst with the activity, accuracy, and dual functionality (enzyme and template) of an RNA replicase would be so rare that it could only arise spontaneously and in a single step from a truly enormous amount of RNA. The problem is compounded because two such sequences would be required for autocatalytic replication to begin, one to act as the polymerase and a second to act as the template. Therefore, an RNA replicase could only have arisen from primordial sequence pools that were not truly random. Joyce and Orgel anticipate this difficulty and propose that nonenzymatic, template-copying reactions may have had a dual role in generating primordial sequence pools that are more likely to give rise to a replicase (21). The initial pool may have been biased in favor of local secondary structure by a mechanism involving intermittent use of intramolecular sequence as the template. In addition, some sort of nonenzymatic catalysis was probably necessary for the initial copying of the replicase sequence to generate a molecule that could be used as a template, the copying of which by the replicase would generate more replicase molecules, thus initiating the autocatalytic explosion of life.
[...]
The ribozymes that we have selected provide a new starting point for the evolution or design of RNAs with RNA polymerase and replicase activity. A series of issues including sequence-independent primer-template binding, the use of mononucleotide triphosphates as substrates, fidelity, and product-template dissociation now need to be addressed before an RNA replicase activity, an activity that has probably been extinct for over 3 billion years, can be fully resuscitated.

Johnston et al. (2001) took this experiment even further: starting with a pool of slightly mutated ribozyme ligases developed in a previous SELEX experiment, they were able to generate a ribozyme polymerase. This polymerase was able to catalyze the addition of nucleotides to a growing oligonucleotide chain up to 14 bases long and based off of an RNA template. The polymerase was also quite accurate.

(Johnston et al., 2001); Excerpts from the in vitro evolution of a ribozyme polymerase.

However, the authors are skeptical of this being the sole mechanism behind the rise of an autocatalytic ribozyme:

How could general polymerase activity have arisen on early Earth? If emergence of the first RNA replicase ribozyme coincided with the origin of life, it would have had to arise in a single step from prebiotically synthesized RNA, without the benefit of Darwinian evolution. Our shortest construct retaining activity was 165 nt, with about 90 nt involved in important Watson-Crick pairing and at least another 30 critical nucleotides (23). Ribozymes with the efficiency, accuracy, and other attributes of an RNA replicase might have to be even larger than this. However, current understanding of prebiotic chemistry argues against the emergence of meaningful amounts of RNA molecules even a tenth this length (1). This difficulty is anticipated by those who propose that life, and Darwinian evolution, began before RNA. Some speculate that in this "pre-RNA world," life was based on an RNA-like polymer, yet to be identified, that possessed the catalytic and templating features of RNA but also a more plausible prebiotic synthesis (1). The pre-RNA life forms presumably later developed the ability to synthesize RNA, facilitating the emergence of an RNA replicase ribozyme, which in turn enabled the transition to the RNA world.

There are other, similar experiments where people have made self-replicating ligases (Paul and Joyce, 2002) or a system of two, cross replicating ribozymes (Lincoln and Joyce, 2009). While the question still remains unanswered, perhaps from all of this you can get a sense of the plausibility.
References:

Bartel DP, Szostak JW. 1993. Isolation of New Ribozymes from a Large Pool of Random Sequences. Science. 261(5127):1411-1418.
Ellington AD. 1994. Aptamers achieve the desired recognition. Curr Biol. 4(5):427-429.
Johnston WK, Unrau PJ, Lawrence MS, Glasner MR, Bartel DP. 2001. RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension. Science. 292(5520):1319-1325.
Lincoln TA, Joyce GF. 2009. Self-Sustained Replication of an RNA Enzyme. Science. 323(5918):1229-1232.
Paul N, Joyce GF. 2002. A self-replicating ligase ribozyme. P Natl Acad Sci USA. 99(20):12733-12740


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List of Asymmetric Animals
The (male) Fiddler Crab is a famous example of an animal whose morphology exhibits neither mirror nor radial symmetry:

(Image source)

List of animals featuring external asymmetry is a Wikipedia article showcasing a few more animals with this property.
Is there a comprehensive list of all such animals that have been described?

Many(all?) sponges are asymmetrical.

I don't think that there is a list yet for all but I could probably help you with a few if that is ok.

Any that are not on the Wikipedia list would already be helpful :)

I am asymmetrical. My right hand is bigger than my left. :)

There is a Wikipedia page called "list of animals featuring external asymmetry"

1) Pareas iwasakii has asymmetric mandibles.  A few more examples of asymmetric snakes (reference)

Pareas iwasakii skull
2) Camels have an asymmetric penis (reference)
3) You could find quite a few in this article titled Animal asymmetry
Hope that helps. I am sure there are more but these are some I could find.


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What Proteins Are Universal To All Life Forms?
According to National Geographic, there are 23 proteins that are common to all life forms:

All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains

According to NCBI there are 324 proteins common to all life forms.
How many proteins are common to all life forms, and what are their names?

It must be 23 amino acids. Amino acids are structural units of proteins. Can you cite the material that said 23 proteins are common to all life forms?

what do you mean by common.. there are homologous proteins.. would you consider them as common?

There are 324 proteins in M. jannaschii, with at least one homologue present in some species from both the other two domains, Bacteria and Eukarya ..... I don't think the NCBI article you cited is talking about proteins common to all life forms.

I am skeptical about 324 as well because an organism named Tremblaya princeps apparently has only 120 protein coding genes. http://www.nytimes.com/2013/07/04/science/how-simple-can-life-get-its-complicated.html?_r=0

I would have thought Ubiquitin would be in the list, considering its derived from the word ubiquitous.

This question is based upon a wrong inference about the work that forms the basis of the National Geographic article, which includes this statement:

All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains (quick genetics overview).
  The 23 universal proteins perform fundamental cellular activities, such as DNA replication and the translation of DNA into proteins, and are crucial to the survival of all known life-forms—from the smallest microbes to blue whales.

The article is referring to a paper published in Nature in 2010.
http://www.ncbi.nlm.nih.gov/pubmed/20463738
This paper uses a set of 23 proteins to test the idea that certain genes arose only once.

The data set consists of a subset of the protein alignment data from ref. 27, containing 23 universally conserved proteins for 12 taxa from all three domains of life, including nine proteins thought to have been horizontally transferred early in evolution27. The conserved proteins in this data set were identified based on significant sequence similarity using BLAST searches, and they have consequently been postulated to be orthologues.

There is no suggestion that there are only 23 such proteins, it's just that the author chose this subset to test his ideas.
And here they are:

alanyl-tRNA synthetase, aspartyl-tRNA synthetase, glutamyl-tRNA synthetase, histidyl-tRNA synthetase, isoleucyl-tRNA synthetase, leucyl-tRNA synthetase, methionyl-tRNA synthetase, phenylalanyl-tRNA synthetase β subunit, threonyl-tRNA synthetase, valyl-tRNA synthetase, initiation factor 2, elongation factor G, elongation factor Tu, ribosomal protein L2, ribosomal protein S5, ribosomal protein S8, ribosomal protein S11, aminopeptidase P, DNA-directed RNA polymerase β chain, DNA topoisomerase I, DNA polymerase III γ subunit, signal recognition particle protein and rRNA dimethylase

This answer was downvoted - I'd be really interested to hear why.


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Why are we carbon-based?
Is that because of evolution?
Does it have something to do with its amount in the universe?
Carbon compounds form the basis of all known life on Earth, and the carbon-nitrogen cycle provides some of the energy produced by the Sun and other stars as I know.

related post

The definition of life as of now requires carbon based compounds(proteins,DNA etc). It's almost essential to the definition of life as of now. If there are other forms of life(possible) based on other macro molecules built using a different element from the periodic table, we could understand better why we are carbon based. Right now people say its because carbon can form chains to form proteins, but why do that? Is there no other alternative? If you think about it, the current(no consensus) definition of life is based upon the fact that we are carbon based.

We are carbon-based because carbon is the only molecule that is able to form the long, long chains of hundreds of molecules that are required to from proteins, DNA, etc. Absolutely no other molecule will do it. (Whatever you may have heard on Star Trek about Silicon-based life, Silicon doesn't form chains anywhere near as long.) Plus it's very handy in that its oxide is carbon dioxide, which is a gas, so using it and oxygen (another gas) as the end-points of respiration is very handy, you can get rid of a lot of gas very quickly. Silicon's oxide is, well, glass.
If you want to know why only carbon forms long chains, it's because of its size (not too large like silicon), its medium electronegativity (it's in a middle column of the periodic table, so it forms what are called "covalent bonds" very easily, especially with hydrogen, the #1 element in the universe by far; covalent bonds are easy to form and easy to break) and its valence (again, because of its position on the periodic table -- it forms four bonds, the maximum for a smallish molecule, giving it the geometry to form long chains).
For life to be based on anything but carbon, it would have to be made only of smaller molecules, which to our knowledge isn't very likely. Our DNA molecule is made up of billions of atoms; it's difficult to conceive how heredity could work on a small scale.

would be nice if you bothered to give references to your answers by which people interested to get more info could read full articles.

Another factor is relative abundances of different elements in the universe.

@The Last Word, all of that stuff is pretty easy to find via google (once you know what terms to look for), I'm sorry, I don't have the references handy, it's all pretty basic background knowledge to people who are familiar with these things. I took time out of my life to answer a question, I'm sorry if you feel I didn't do enough.

@WYSIWYG, you are absolutely correct in that if carbon were not so abundant, there would be no life as we know it!

I just pointed out something that you do on stackexchange to validate answers. Everyone does it and Iam in no way belittling your effort. I noticed that you do most of ur answers without references and if u feel Iam being overbearing I take it back

That's okay, it's just the word 'bothered' that took me aback a bit, but I'm over it. AFAIK, in general you don't put references to basic and easily verifiable information. (This is not an insult to the question, what's basic to someone is not to someone else, and you have to know enough to know how to phrase the question). If I were putting things that were only found in a handful of sources, definitely I'd put a reference. I'm new to StackExchange, so maybe the bar is set lower than I'm used to? What do you think in my response most needs a reference?

Too long for a comment. Just extending the answer from @prooffreader slightly.
It's true that long carbon chains are present in lipids, but in proteins and nucleic acids there are chains of carbon atoms interspersed with other atoms:
nucleic acids: -C[3']-O-P-O-C[5']-C-C[3']-

protein:       -C[alpha]-C-N-C(alpha)-

So the ability of C to form stable bonds with N and O (and S) is also important. It is also important that these bonds with heteroatoms are not too stable, thus allowing for making and breaking bonds at physiological temperatures. Then add to this the fact that most carbon atoms in biomolecules are tetravalent so that even when they are part of a chain they can be linked to other functional groups 'hanging off' the chain (such as amino acid side chains).
This combination of properties is unique to carbon.

Thanks for pointing that out, I wasn't clear in my resonse, I didn't mean carbons form long chains just with each other, but every long biomolecule chain involves carbon, there's no other element that's in every biomolecule chain bond).


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How much DNA of Albert Einstein is recoverable?
Since there seem to be five biological descendants of Albert Einstein, and the original chromosomes of him distributed among them ...
Is it possible to recover enough DNA of an individual from his progeny and proceed to clone him? Any information would be helpful

I've edited the first part of your Question because what to do there seemed obvious.  However, I would rather leave the remainder for Biology SE to address.

Technically I think not even if his own children were alive but I am very interested in an answer.

A large chunk of Einstein still exists (pickled brain) and protocols exist to recover DNA from formalin fixed tissues.  It wouldn't be easy, but in theory, you could derive its full sequence and synthesize artificial chromosomes for cloning.

During the generation of gametes (sperm, eggs), chromosomes can cross-over - this swaps paternal and maternally-derived genetic material.  So none of the descendant's chromosomes would be a direct copy of Einstein's, and furthermore, each offspring receives half of its genetic complement from each parent.  This means that if you pool the DNA data from small number of offspring you may not obtain all the elements of one parent's DNA or be able to assign that data back to a specific 'original' chromosome. (On top of this you would have to determine which sequences in the offspring came from the other parent).
If I was cloning Einstein, I'd use his DNA.  Is his comb in a museum ? A tooth? A letter he licked?  A large chunk of Einstein still exists (formalin fixed brain) and lab protocols can recover DNA from formalin fixed tissues. It wouldn't be easy, but in theory, you could: i) derive its full sequence and ii) synthesize artificial chromosomes with suitable epigenetic modifications, and iii) inject those into enucleated eggs for human cloning or iv) transfect them into enucleated cells from a cell line, make iPSCs and then fuse those with ~8-cell fertilized embryos.
(Spoiler - not technically do-able today and almost certainly illegal in most states/countries).
For a related movie treatment, the Boys from Brazil  tells a good story - warning Nazi content.

thanks a lot for your attention to my question , and the illegality of this work is amazing !

i) and ii) will probably never be impossible due to genomic regions that cannot be sequenced, un-resolvable epigenetic statuses and the major difficulties in synthesising ekaryotic chromosomes. Nice thought experiment, though.


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What E-value BLAST cut-off is best?
What is the best cut-off for e-value in BLAST?
Some say 0.01 ,others 0.0001?
Even BLAST tutorials don't give a very clear idea about which cutoff suits which purpose?
Could some experts give me a clear idea on this.
Why are we using 0.0001 and not 0.00011?

There's virtually no difference between 0.0001 and 0.00011; cutoffs work in orders of magnitude. Depending on what I'm doing, sometimes I'll use 0.1, sometimes I'll use 1E-30 (0.000000000000000000000000000001).

Honestly, e value means very little and is hard to judge. Its often case dependent

For nucleotide alignment use 1e-05 --> http://pathblast.org/docs/e_value.html

There is no perfect cut-off. It always depends on what you're doing. The e-value is basically a measure of how many such alignments you would expect to find in a database this size by chance. Therefore, e-values greater than 1 mean that you'd expect at least one alignment similar to what you've found by chance alone.
As others have stated, the e-value is not a rigorous measure of significance. It depends on

The length of your alignment.
The alignment's bit-score score (this takes into account amino acid substitution scores based on the matrix being used, BLOSUM65 by default).
The size of the database you are searching in.

I have at different times and for different projects used e-values ranging from 10 to 1e-100 or less. You always need to take into account what you are looking for. For example, to run a tBLASTn looking for distant homologs, you'd use a relatively high e-value, say 1e-10 or even 1 or greater depending on the details. For example, the default e-value for ncbi-tBLASTn is 10.
To find extremely similar sequences in closely related species, you'd use a much smaller one. Say 1e-20 or 1e-50. Normally, you tweak these settings after seeing your results.
After running a few hundred blasts, you get the hang of it and you can have a pretty good estimate of the e-value cutoff you want to use. Until you get that experience, you will have to use trial and error. Just remember that the conclusions you can draw from your data will be heavily influenced by that e-value. Don't try to publish something claiming you've found a homolog if the supporting BLAST hit has an e-value of 45 for example.
Personally, when looking at BLAST out files, I check the e-value, the alignment's length (as a percentage of the query), the alignment's %id score and the bit score itself. Of these, the most reliable is the bit-score but, again, that too changes depending on what question you are attempting to answer.

@OP I would also add this point that the cutoffs, scoring schemes and inferences are dependent on what you really want to find. It is to be first reasoned if BLAST is the right tool for what you are seeking.

The e-value is supposed to be a metric for the chance that an alignment could occur at random, but it is a crude estimate.  As pointed out in other answers, this significantly does not include the length of the query sequence.
It also does not include the conservation of the gene or the frequency of amino acids (in protein blasts).  It does take into account the database of sequences queried, which might be something you know very little about if you didn't make it yourself.
That being said, 1e-5 is a pretty poor score.  Its really awful for nucleotides - maybe a perfect alignment for 10 or 12 bases. So I'm going to assume that you are looking at peptides.
You should also look at the coverage statistic.  That is the length of the alignment divided by the query or the hit sequence.  It should be 70%+ depending on what you want.
If the coverage is good even answers pretty far down the score rankings might be relevant.
Similarity is usually performed with a BLOSUM matrix.  Regardless, the number of exact matches compared to the number of similar matches of amino acids in an alignment poorly approximates what is going on in evolution.
Lastly protein alignments tend to have gaps - lots of gaps.  The penalty to the scores for allowing gaps might low for long evolutionary distances or completely unreasonable for more recently diverged results.  So you have to look at those qualities of the alignment yourself.

"It does take into account the database of sequences queried, which might be something you know very little about if you didn't make it yourself."
This is incorrect. Database size directly affects E-values.

@5heikki.. what are you refuting here? Both the statements mean the same thing...

Sorry but this is really not correct. As explained in the page you link to, the e-value is given by E=Kmne^λS where S is the alignment's score. Since this is a measure of (among other things) the conservation of the two sequences, the e-value includes both "conservation of the gene" and "the frequency of amino acids". Also, to my knowledge, all popular BLAST implementations (and certainly ncbi and wu-blast) use BLOSUM65 matrices, not PAM by default. In fact, I don't know of any program that uses PAM matrices by default and I can't imagine why you would want to.

http://en.wikipedia.org/wiki/Point_accepted_mutation#Use_in_BLAST

CLUSTALW uses PAM and BLOSUM both.. It is preferable to use BLOSUM for local alignments and PAM for global alignments.. Makes intuitive sense, thats it; no hardcore reason..

Thanks for the edit. Note that the wikipedia article you posted cites the same ncbi link you have in your answer which also states that "A number of tests suggest that the "BLOSUM" matrices produced by this method generally are superior to the PAM matrices for detecting biological relationships." Essentially, PAM have been replaced by BLOSUM.

E-value refers to the expected number of random hits for a given alignment score. Smaller it is more reliable is your match. There is no hard and fast rule for e-value cutoff. You can keep whatever you want depending on the level of stringency that you require. But you should note that for smaller sequences (< 30nt) there is always a higher likelihood of random matches. In such cases it is practical to relax the e-value cutoff.

The E-value of 0.0 indicate the number of alignments with scores equivalent to or greater than that are expected to occur in a database by chance therefore the lower the E-value the more significant the score hence a better quality of the alignment blast search.

can you share a reference that others can read for more information on your answer? it would definitely strengthen your answer - thanks for your contribution!

A score of 0.0 zero isn't actually zero it's just lower then 10^-100

The e-value is required to have confidence in the hit, along with hit. Generally, an e-value of e-4 is preferred because, this cutoff is found to be sufficient enough by blast to confirm a hit as homolog. But, for a hit, an e-value greater than e-4 does not mean it is a homolog neither we can say it is not a homolog. We cannot surely infer anything from these hits. Therefore, researchers choose a value

There is no magical threshold that defines homology! It depends completely on the specifics of your situation. There are cases where you can find true homologs and an evalue >10. Everything depends on the length of your sequences, the size of your database, the conservation of your homologs etc.

Sorry if my answer seems confusing. But, is it not that an evalue much closer to zero is considered homolog? Because, i see in some papers and tutorials using e-4 or lesser value to assess homology as a rule of thumb. Those hits, where the evalue > 10 may or may not be a homolog, but i think we cannot definately say they are homolog, without further insights. Would like to hear your comments. Thanks.

No. We can never decide on homology based on the e-value alone and there is no single magical threshold. The threshold you choose will always depend on the particular question you are asking (how diverged are the species? How long is your sequence? How large is the database? Is this nucleotide or protein blast? etc). What is important for deciding homology is the particular regions of a sequence that are conserved (e.g. domains). For example, if you search for a homolog of a very short sequence with repetitive regions, you will never have a small e-value.


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Loss of allelic variation per generation of full-sib mating
If we take a male and female, cross them, and collect one son and one daughter to produce the next generation (and continually do this for many generations) - (full-sib mating design) how much genetic variance is lost per generation/how do we calculate this?
Assume all sites initially have allelic variation, and we imagine a diploid sexual species.

A classical result from the Wright-Fisher model of genetic drift is that at each generation the heterozygosity ($2x(1-x)$) is expected to decrease by $\frac{1}{2N}$ due to genetic drift. ($x$ is the frequency of one of the two alleles). In your example the expected loss of heterozygosity is $¼$. This same result has been derived from coalescent theory and a similar result is derived from the birth-death Moran model. The issue is that this model assume bi-allelic loci only.
Let's think of 1 tetra-alellic (4 alleles) locus and let's assume that the 4 alleles in our two original parents are all different. We can draw the 16 possible pairs of offsprings and see the probability to lose 0, 1 or 2 alleles in the next generation
lose 0 allele: ¼
lose 1 allele: ½
lose 2 alleles: ¼
lose more than 2 alleles: 0
Therefore, the expected number of lost alleles is $1$!

We can then do the same (calculate the probability mass function) for two parents with 3 alleles and then 2 alleles (with various frequencies). It is not very complicated. But it would be much better to have a general model to describe the loss of heterozygosity through time for more than 2 alleles. This paper probably gives this solution but I haven't read it yet. I will probably read it once and I will improve my answer then!


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Is there any evidence for secondarily poikilothermic vertebrate?
Is it possible that an endothermic physiology can evolve into an ectothermic (poikilothermic) physiology? I have a non-scientific gut feeling that it is irreversible. Whales and dolphins are evolved from land mammals, and they've remained warm blooded. While it doesn't give them any obvious advantage in the water, apparently they've compensated with massive amounts of body fat instead of devolving. If the ocean offers opportunity for mammals, then why haven't fish evolved to be warm blooded directly?

You may want to use a term other than devolve. http://en.m.wikipedia.org/wiki/Devolution_(biology)

What do you mean by cold-blooded?
There's an issue with what you mean when saying "cold blooded". The correct words you may want to use are homeotherm, poikilothermic, ectotherm, and endotherm. In short…
Source of heat

endo = inside
exo = outside

Variance in warmth

Poikilo = varies
homeo = does not vary

Any combination of these two axes exist. For example: If the temperature in the environment never varies you can be homeotherm without needing to be endotherm. A fun example also are the large dinosaurs that are thought to be homeotherms because their metabolism produce some heat and they are so large that they remain warm thanks to this heat source. However, they were probably not able to regulate actively their temperature. Therefore, I would tend to qualify dinosaurs as homeo-exo-therm but I wouldn't be surprised if someone prefers to call large dinosaur home-endo-therm individuals. Hope that makes sense to you.
Note that the terminology might be a bit more complicated in reality as the diversity of mechanisms of body temperature regulation is important.
What did you mean in your question when talking about "cold blooded" species?
Transition from endothermy to ectotherm
Thanks to @tchrist. naked mole rat is ectotherm while its ancestors where endotherm.

This perfectly makes sense so far and what I tried to ask exclusively is if there is an example of a mammal that devolved to an ectotherm. But appearantly the transition that I'm looking for isn't really obvious. I would still be interested in any potential example though.

With "cold blooded" species I meant to say ectothermic species, but I wasn't familiar with those scientific terms yet.

@user43058 I don't think there is any ectotherm mammal. Some have important variation in temperature during hibernation though. The question of the benefits and costs of being ectotherm verus endotherm and how endothermy can evolve - is very broad. And it is a very interesting question! I encourage you to ask this question in a separate post. I had a lecture on the subject during my Bachelor degree, I personally may be able to help you on another post if I go back to this lecture.

The naked mole rat (Heterocephalus) has some rather odd thermoregulation characteristics for a mammal.

@tchrist Indeed, according to wiki the naked mole rat is the only mammal ectotherm. Thanks


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Is it possible for neurons themselves to manifest cancerous behavior?
From what I understand, one form of cancer is a faulty gene responsible for the programmed death of a cell.
Not long ago, popular wisdom used to say neurons don't regenerate. However that is no longer believed to be true, if I am to believe what the internet says. For me, this begs the question: can neurogenesis result in faulty death genes which in turn result in overgrowth of the number of neurons? Would those neurons be functional? And if so, if theoretically such a brain could be artificially sustained without a body, would its growth be beneficial (in terms of intelligence)?

Yes, but rarely.
Other types of brain cells are much more likely to form tumors. Oligodendrocytes, astrocytes, and more generally glial cells all form tumors with some regularity.
Nerve sheaths can also form benign growths.
Nerves themselves can even manifest cancerous behavior, even though they are nearly always benign and very slow growing. Unfortunately, they tend to cause seizures, increased intercranial pressure, and decreased neurological function in affected areas.


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What is the purpose of back-crossing mice for multiple generations?
Occasionally I will come across articles that refer to back-crossing mice of one strain onto the background other another strain (e.g., C57Bl6). They do not explicitly state the purpose for doing so, but I can infer that the change of strain is to relate their findings to what is already known using the new strain (e.g., C57Bl6). Usually the back-crosses are performed for 5-10 generations. Is this to try to remove (epi)genetic variation from the original strain relative to the new strain, or is it more about normalizing expression of a particular allelic variant (e.g., knocking-in a transgene)?

I'm no expert at this (and take this comment with a very large pinch of salt!!) which is why I leave this as a comment. The only reason I know of in other species such as Drosophila and C.elegans that you back-cross this much is to dilute out all the other potential mutations, insertions etc until you are only left with the mutation that you are interested in. This often happens with P-element based mutagenesis but again take this with a very large pinch of salt!!

Depending on the exact goal of the experiment, the researchers may back-cross both to smooth out genetic variation between individuals and to potentially normalize expression of a transgene, although once you get past the chimeric stage gene expression should be fairly stable. In my experience, back-crossing allows you to generate a genetically-altered mouse that differs as little as possible from a (generally well-characterized) parent strain, except at the locus of the genetic manipulation. This way, any differences in phenotype can more easily be explained by the knockout/knockin/transgene/what-have-you, and not by any variations in background genetics.
As an example, C57BL/6 mice, being inbred, have a number of well-known mutations, deficiencies, resistances, etc., and for one reason or another have become one of the most popular and most-characterized mouse strains in biology, so there is a great interest in continuing research using a well-known historical model with so much extant experimental data. These mice are quite different from the 129 strain, which are frequently used to make initial genetically modified strains due to the large number of embryonic stem cell lines available, and other technical reasons which allow for the relatively easy generation of transgenics, etc. However, for various other reasons, 129s aren't used as often in the type of studies that BL/6s are, so it's preferable to create the mutation in a 129, then back-cross it onto a BL/6 background. Both of these strains are quite homogenous from one individual to another (each sibling is practically a twin of the next), but once you start breeding 129s to BL/6s you can generate all sorts of genetic heterogeneity due to random cross-overs and all the other things we like to talk so much about around here when it comes to mutations and meiosis. As anyone who has worked with genetic diseases in humans will readily tell you, it can be extraordinarily difficult to nail down specific genotypes that lead to specific phenotypes when there are so many other confounding factors present. Backcrossing a mutant 5, 10, or even 20 or more generations back onto a reference strain is one of the best ways we have at the moment of controlling for all the genetic variations that are introduced when two inbred "tool" strains are bred together.
And now, cute pictures :)
129 mouse

C57BL/6 mouse

both images from Charles River


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Can a heterozygous allele show non-heterozygous expression in a family?
I'm doing a family study looking for novel cancer-associated variants in germ-line samples; the goal is to find candidate biomarkers which might be used for early detection. At an earlier step our analysis, we eliminated a family that showed a heterozygous mutation known to be associated with our cancer under the premise that this known mutation better explained the presence of the disease than any novel variant we may have found.
I've now found another mutation, strongly associated with out cancer, which we does not appear to be heterozygous. 2 out of 3 family members share this mutation with a within-family allele frequency of 0.5.
Trying to decide whether this means I need to discard this family from further consideration, adjust my thinking, or not worry about it. My current thinking is that it'd be safest to eliminate the family from consideration because the mutation pathogenic and found in the germline but I can't wrap my head around how the lack of a heterozygous pattern affects things. Does it absolutely mean the variant was not inherited? Can anyone help me get my thoughts straight?

I don't really understand your question. Basically at a given bi-alleleic locus, you have one allele that you suspect to cause cancer. In your sample (not only in one family), this locus in never found in the heterozygous state? And you ask "how is this possible"? Did I understand your question? Have you performed a chi-squared test (or test based on a binomial distribution) in order to test whether the lack of heterozygosity is really unlikely to happen by chance?

One of the fundamental premises of this project is that the families we are looking at do not have heritable mutations known to cause cancer (at least not the cancer we're interested in). We eliminated one family from consideration because they showed such a mutation in all members with an allele frequency = 0.5; My question is whether I should eliminate this second family in which 2/3 members have the known, cancer-causing variant for being useless


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Can (any) human cells learn?
I'm not talking about single celled organisms, but actual cells in your body. Is there any evidence that they can learn to, say, navigate an environment or avoid an aversive stimulus like an animal could? Is their behaviour understood well enough to say that it's entirely mechanistic, or are there things we still don't know?

I'm not entirely sure what you're asking. What do you mean by "learn", and are you proposing a situation where the cells have somehow become removed from the body?

you can start by reading on acquired immunity. http://en.wikipedia.org/wiki/Adaptive_immune_system

yes they do.. what do you think the epigenetic mechanisms are for.. 8-)

@MCM yes - I'm thinking along the lines of classical conditioning.

Memory B cells learn the molecules of the pathogen?

For this specific question, let's divide the cells into two categories:
Cells that rarely "navigate" are the cells that are connected to give the tissue its mechanical properties. How do these avoid an "adverse stimulus"? Well, they don't avoid it. But if that stimulus "harms" cells they react in some way:

if the cell is destructed by the pathogen, it will release chemical compounds that have chemotactic properties and attract specialized cells.
if the pathogen has intracellular tropism, the cell may release some chemical compounds (see interferon) to "alert" other cells that something is wrong. Most cells can also present antigens on their surface.
there are also some stimuli which change cellular life cycle turning cells into cancerous cells. These cells can gain excretory properties and produce substances that destroy intercellular jonctions. This is how metastases occur.

Cells that "navigate" are the blood cells. White blood cells respond to different kind of stimuli (chemical) in two ways: either they are attracted (by inflammatory cytokines for example) either they are repelled. Macrophages are attracted by cytokines released when a pathogen agent triggers inflammatory response. They "ingest" that pathogen through phagocytosis and expose some parts of it (the antigens) on their surface receptors. This stimulates lymphocytes which process that antigen and decide if it is self or non-self. If it is non-self, they stimulate proliferation of specialized cells against that antigen. Another type of blood cells, the platelets, although they have no nucleus, have interesting properties: they can adhere to the broken endothelium where they change shape and start to produce different chemical mediators.

Read more on:

Wikipedia contributors, "Chemotaxis," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Chemotaxis&oldid=600637322 (accessed June 28, 2014).
Wikipedia contributors, "Interferon," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Interferon&oldid=608718450 (accessed June 28, 2014).
Wikipedia contributors, "Adaptive immune system," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Adaptive_immune_system&oldid=612379171 (accessed June 28, 2014).
Wikipedia contributors, "Platelet," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Platelet&oldid=614627651 (accessed June 28, 2014).


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Can skin become denser?
I heard that after injury or repeated damage bone becomes denser, can skin become denser as well?

refer this question http://biology.stackexchange.com/questions/8687/is-it-possible-to-condition-the-body-to-reduce-bruising/17904#17904

a large part goes to the type of injury inflicted, eg: sun damage makes it wrinkly and weak while repeated injury could cause the accumulation of dead cells reducing sensitivity.

The structure of skin (epidermis) can change with damage, when the skin is broken the body repairs this partly by recruiting cells called fibroblasts. These fibroblasts lay down collagen fibres to repair the skin. These fibres a normal component of skin are not as neatly arranged as the original fibres and may also higher in number leading to 'denser' skin. This is essentially what a scar is. In some cases the above process can go awry forming what is known as keloid scars.
The other thing that can happen with repeated pressure exposure the skin can become callous, this is when there is thickening of the outer layer formed of cells called keratinocytes increase in number due to recurrent damage. These form typically on pressure points such as balls of feet.


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Calibration curve for single radial immunodiffusion
When we draw a calibration curve for single radial immunodiffusion, the curve does not pass through origin. Instead, there is a y intercept. Why does that happen ? Shouldn't zero antigen give zero ring diameter ?

When the radial immunodiffusion method is used to measure antigen concentrations in samples, a plate or slide is set up using agarose containing an antibody or antiserum. Holes are punched out of the agarose to form wells into which antigen is dispensed. The antigen diffuses out into the agarose and when the antigen/antibody ratio is favourable an immunoprecipitate will form as a ring (immunoprecipitin ring). The final diameter of the ring is proportional to the initial concentration of antigen.
Addressing the question: isn't this simply explained because the values on the Y axis are squares of the diameters of the rings, and this includes the well into which the antigen is dispensed?

Thanks ! I thought the diameters were taken from edge of the ring.


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How does the Cuttlefish camouflage itself accurately despite being color-blind?
I have seen/read that the Cuttlefish is able to camouflage itself extremely accurately. I have also seen/read that they are completely color-blind, though see with very high contrast. How does the Cuttlefish manage to blend itself so well to its changing surroundings if it is not able to perceive the colors it is changing itself to?

Plants have evolved coloured flowers which they cannot see. Insect mimics have evolved patterns of colour which they cannot see. If the phenotype offers an advantage it can be selected for. Presumably cuttlefish can use other sensory cues to determine the nature of their surroundings and this information can be used as an input into the chromatophores and iridophores.

@AlanBoyd indeed but since the cuttlefish changes as a function of its environment, it must have some sort of sensory apparatus that can "see" the colors. Whether this happens at the cellular or the organismal level is another matter and what I hope this question might answer.

@terdon I'm suggesting that there is no need to see the colours. If other (strictly non-visual) sensory inputs are an indicator of lying on a sandy surface then these could be used to promote the "correct" choice of colours.

The reason why the cuttlefish is colour blind is because

it just has one type of cone cell. Humans have three different types,
  each sensitive to a different color of light. With only one cone type,
  you couldn’t differentiate between different colors (reference).

A study was conducted in the lab of Dr Lydia M. Mäthger where two different checkerboards were used to test their colorblindness.

1) Gray – Green. One green shade, matched to the maximum absorption
  wavelength of cuttlefish, was combined with 16 different shades of
  gray. As supposed some shades of gray couldn’t be distinguished from
  the green by the cuttlefish, which didn’t adapt the body pattern.
  Experiment one was successful.
2) Blue – Yellow. A checkerboard of blue and yellow matching in
  intensity was used for the second experiment. The skin color of the
  test species didn’t change either and therefore experiment two was
  also successful (reference).

These experiments concluded that it was indeed colourblind.
To confirm the effectiveness of the camouflage, HyperSpectral Imaging (HSI) was used to measure the colour match between the cuttlefish and its background. Using this technology it was perceived as to how a predator would view a camouflaged cuttlefish. It was found that

Cuttlefish can produce color-coordinated camouflage on natural
  substrates despite lacking color vision, and that the color aspect of
  cuttlefish camouflage is highly effective against fish predators. Much
  of the contrast information (which allows a predator to "pick out" a
  cuttlefish from the background environment) resides in the brightness
  (luminance) rather than in the color (chromatic) aspect of the
  reflected light. What this means is that cuttlefish camouflage
  strategies take away a tool from predators in their ability to pick
  out their prey from the background and instead leave them with only
  brightness as a method for prey identification (reference 1 and reference 2).

And now we get to the main question as to how they do it. Cuttlefish are apparently able to detect the intensity of light reflected from objects in its surroundings. It is able to perceive even a 15% change in contrast. In an experiment, it was found that

The animals did not respond to the checkerboard pattern when placed on
  substrates whose color intensities were matched to the Sepia visual
  system, suggesting that these checkerboards appeared to their eyes as
  uniform backgrounds (reference).

In another bit of interesting research done on the ability to copy the patterns on checkerboards (reference), three inferences were drawn

The first find was that the range (relative to the size of the
  cuttlefish ‘white square’) for the animal to exhibit disruptive skin
  patterning had to be withing a certain  narrow range. Secondly, given
  the appropriate size of checker, cuttlefish regulated their disruptive
  skin patterns according to the contrast between white and black
  squares. Third, by manipulating the number of white squares on a board to just  4
  among 316 black squares (or 1.25 %) produced disruptive patterning,
  yet increasing the number of white squares to 20, 40 or 80 did not
  increase the frequency of appearance of the cuttlefish ‘white square’,
  but only its clarity of expression.

This study shows that the number of white objects in the background significantly influence cuttlefish skin patterns further putting stress on its ability to view the polarization of light (reference).

Some cuttlefish camouflage examples

This is a standard answer from @TheLastWord; A very good answer showing an impressive amount of work with many references! Good job +1


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A question on ImageQuantTL
I am confused about using the ImageQuantTL application as a tool to analyse the Urea Gel. My problem is that I am not sure if the 'shape' for calculation should be the same for all samples (like on picture A) or as close to the band as possible (like on picture B)? And what about the background subtraction? The `Image Rectangle/Ellipse' option says:

Uses the average pixel intensity in a defined rectangular or elliptical area of the image. To define the area for background calculation, select the background shape in the navigator and then drag with the mouse. Background areas are identified by a broken colored border, and are numbered in the sequence in which they are created. If you have defined several background areas, select the area to use in the Parameters tab.

Does it mean that the shape for the background subtraction not necessarily has to be exactly the same size as the shape for the band? (See Figure C.) I attach some pictures for your convenience.
Thank you very much for any help.

I would definitely go for option A. If you are assuming that the staining in band 6 is all due to whatever you are measuring, there is no reason to think that the signal at the top of lane 1 is not meaningful.
That said, this type of measures is only semi-quantitative, so being too "picky" in how you choose your region probably won't really increase the precision of your result. If you want to get a quantitative measure I am afraid you will have to turn to some other technique.
Finally note that the area obviously means a lot if you are looking at total intensity of the bands, rather than average intensity.

I can only agree to tihs answer. Be careful with too "exact" measurements here.


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Investigating rare variants in ethnically different populations (European ancestry & African ancestry)
If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) especially considering that the populations have different allele frequencies. Is the main object to see if they're could possibly be novel rare variants in each population at different allele frequencies?

Mainly you do this because these populations have segregated long time ago and developed differently. You will find rare SNPs for pigmentation in europeans that are not present in the more ancient african population (and must therefore be occured after the populations divided), examples are the so called "golden mutation" in SLC24A5 (rs)

Too long for a comment, but sort of:
Mainly you do this because these populations have segregated long time ago and developed differently, so it is more likely to identify these polymorphisms. It is also helpful to use populations for this which mixed not too much with other populations (thats why north-americans are usually not used here, as America was kind of a melting pot).
You will find rare SNPs for pigmentation in europeans that are not present in the more ancient african population (and must therefore be occured after the populations divided), examples are the so called "golden mutation" in SLC24A5 (rs1426654) or a polymorphism in IRF4 (rs12203592).


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will an earthworm survive after covering its skin with a wet cloth
I am very curious about this question. I got this doubt when I was studying anatomy and physiology of the earthworm Lampito mauritii. It breathes through its skin (cutaneous respiration) and if we cover its body with a wet cloth and all the necessary external openings are left uncovered (such as nephridia and other genital pores) then will the earthworm survive?

Assuming it still has access to oxygen through the wet cloth, and the moisture content remains constant, I don't see any reason why it wouldn't survive...

i can't get your point do you mean that earthworm will survive that situation

sorry, it was a double negative. Yes, given sufficient oxygen and a steady supply of moisture, the worm should be able to survive quite happily for some time.

but how would it respire in such watery environment ?

If it's submerged, it won't be able to. But, if the environment is just damp, it will be fine. It's the difference between covering it with a soaking-wet paper towel, and one that has been dampened, then squeezed out some.

yes they do.. they survive on damp tissue papers.. I've tried it..

This is one of those speculative questions where you don't have a definite answer unless you specifically experiment and find out for yourself.
It is a known fact that earthworms breathe through diffusion. It has a thin cuticle over its body and requires moist skin which is achieved by a slimy mucous (reference). It is interesting to note that earthworms are also capable of going into a state of hibernation called estivation (in American english) (reference) which helps them maintain a low metabolic state.
Since you are planning to cover it with a cloth, the material of the cloth also matters. It has to be a material with low breathability. For eg: the survivability of the worm would depend on if you were using a wool or a silk cloth to cover it. Here is an article on the breathability of different fabrics (reference).
In conclusion, I would take a guess that it should survive if the material let air pass through and would go into a state of estivation on low availability of oxygen but maybe not die. After all, they are said to be able to survive even in water  if it contains enough available oxygen. (reference).

this might be a different question but what would happen to the earthworm if you dry it using a wet cloth and then at the same instant make its skin wet by applying water ?

@agharehanabbas It would survive again. There should be  a little bit of time and direct exposure to sunlight to get it sun-dried.

but i think that would effect its repiratory rate and doing so continuously would kill him

@agharehanabbas It has the ability to produce slime to stay wet on its own and moreover, you make it wet by applying water as soon as it dries which is hardly enough time to effect its respiration. In my answer I have already mentioned that it is able to survive underwater and also go into hibernation.


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A question on exclusion of study participants for an Exome genotyping array
I'm reading a paper that used whole exome sequencing on an African
 American and European populations to discover novel low frequency and
rare variants associated with lipid levels & the risk of coronary
heart disease.
They used the Illumina Human exome genotyping array that was designed
based on coding variants discovered from sequencing the exomes of
12,000 individuals. Therefore, they selected their participants from a
study who were not among the 12,000 individuals utilized to design the
array .
My question is: Why would they select individuals who were not among
the 12,000 used to design the array? (I'm thinking because maybe it
could produce false positives associations? bias?)

Can you add a citation for this paper?

@Chris the source is from the paper Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks.http://www.ncbi.nlm.nih.gov/pubmed/?term=Associatoin+of+low+frequency+and+rare+coding+sequence+variants+with+blood+lipds+and+coronary+heart+disease

I'll have a look tomorrow, and I have added the link to your post.

When you design the arrays, you need to have probes on the surface complementary to the sequence you want to detect. Depending on what you want to detect, you need to design these probes with known sequence on a known position.
If you want to detect single nucleotide polymorphisms (SNP), then you need a library of known SNPs on your ChIP, which are basically the position of the SNP and the surrounding sequence.
SNPs can be roughly grouped into two subgroups, common (I call them like this) and rare (frequency in the population lower than 0.1%). The problem with this ChIP based method is that it can only detect SNPs which are already known (or at least are located close to known SNPs with which they in linkage disequilibrium). So if you want to detect rare SNPs in your population sample, you need a big group of people from which you take the SNPs into you ChIP design. If you look at the numbers, one rare variant will only be present in about 12 of the 12.000 persons used in the design.
Your study group is then different from the group of people, which where used to make the ChIP design. Here you take people with a certain background (high lipid levels for example) and then compare, if people which had coronary heart problems have SNPs in common which might be connected to this disease. This can help to identify a mutation in a protein which is the risk factor.

authors: Hášíl Páůďýál


text:
Theoretically, what technique would one use to modify a virus so that it only affected a subset of the population?
I'm writing a novel and i would like to know some of the equipment and techniques involved with modifying a virus.
Is it feasible for a virus to be engineered to only affect certain people? It doesn't have to be possible, only sound like i know what i'm talking about. I have been trying to research the subject but nothing i have found will tell me the basics of what is involved with virus modification.
Thanks.

just read http://en.wikipedia.org/wiki/Genetically_modified_virus

What you need to have is a unique entry road for the virus into the body which is specific for your subgroup to be infected. This might be a mutated surface receptor of cells lets say in the respiratory system. The virus can only dock to the mutated version to enter the cells. Changing a virus is some very basic molecular biology combined with cell culture. It will require experience and some specialized lab equipment (to work sterile for example) but can definitely be done.

Just for humour: Are you trying to make a virus that will kill only some selected people that you want to exterminate?? :P

@WYSIWYG Well, his novel certainly looks to be along those lines. :D

Yes, it is possible and probably you won't need many literary artifices to make it work.
Essentially viruses are what is technically called "obligate intracellular parasites".
Parasites because they cannot grow by themselves, they need a host cell from which they "steal" the intracellular machinery to replicate; intracellular because they grow inside cells; and obligate because they cannot reproduce outside their target cell.
Now, each virus has its "favourite cell" to infect. For instance HIV targets a type of lymphocytes (cells of the immune system), other viruses may only target bacteria (these are called bacteriophages) and so on.
How is this specificity achieved? Well, to put it simply, viruses "anchor" to specific proteins (or other molecules) that are sitting on the membrane of their target cells and that allows them to go in. If a cell does not have that specific protein, then the virus cannot infect it.
So, in your story, maybe the target population will have a mutation in their genome that will modify a certain protein. You could then (fictionally) construct a virus that specifically targets cells expressing that protein and you're set!
The virus construction part is just standard molecular biology, really.
A few things to read:
http://en.wikipedia.org/wiki/Genetic_engineering
http://en.wikipedia.org/wiki/Genetically_modified_virus
http://en.wikipedia.org/wiki/Viruses <--this explains a lot

@OP.. you should note that the small differences in these membrane proteins may not be great enough to abolish virus binding. There are few individuals with mutations which will abolish or enhance virus adsorption, although, it is unlikely (considering present statistics) that an entire population is either immune/highly susceptible to a virus. You can claim that a hypothetical virus infects a certain population which has lets say a certain HLA type.

Humor again. In your novel you can name the evil scientist as Chris Nico :P

Also - there would be a strong selection for mutant viruses which gained the ability to recognise the receptor variant in the immune population.

@WYSIWYG Hehehe, nice idea. :-)

@WYSIWYG: sure, sure, but I think that for a novel one can allow a little bit of "relaxation" in how correct is the biology :)

Failed to mention the importance of a viral envelope

@buzrw.. viral envelope is where the adsorption proteins are present. Everything that a virus has is encoded in its genome.. what has anyone missed here?

Please explain if you leave a negative vote so I can improve the answer. I can surely go into much nitty gritty detail about virology, but that will probably not help the OP, but rather confuse him...

@nico that will probably not help the OP, but rather confuse him... OP seems to be a girl :P

@WYSIWYG: oops, sorry kelw, I was lazy enough not to scroll up to the top ;)

Virus is a non-living but infectious structure consisting of a nucleic acid core and envelope covering. The envelope is what determines target specificity.
If you are genetically engineering, lets say a retrovirus (which if you are writing a sci-fi book this is probably the type of virus you are wanting to write about, for many reasons) you would want to use peices of DNA that code for integrated expression cassettes for viral Gag, Pol, and Env proteins, all of which are required in trans to make virus.
These DNA's would be mixed and then put into a living mammalian cell (what we cell biologists call a packaging cell). This packaging cell line transcribes and translates the 3 cassettes and builds the virus.
The gag gene encodes internal structural proteins, pol encodes reverse transcriptase
and integrase, and the env gene encodes the viral envelope protein, which
resides on the viral surface and facilitates infection of target cell by
direct interaction with cell type-specific receptors; thus the host range of the virus is determined by the design of the envelope proetin.
As for some example envelopes, the amphotropic envelope protein has historically been the protein of choice for infection of human and other mammalian cell lines. The 10A1 envelope protein has also been used due to its increased versatility relative to the amphotropic
protein.

As @WYSIWYG mentioned, I think HLA type is probably the best way to claim specificity.  Then the glycoprotein (fusion protein probably) on the virus fits only in an exact MHC class II molecule.  If you want to hit some valid heavy science jargon, I recommend saying the virus was made with recombineering, using a bacterial artificial chromosome (BAC), with a florescent marker to make the scientist's life easier (mush harder to work with viruses without nice markers).
Here is a methods paper that describes that exactly, and has the advantage of of a free published protocol as well.
My problem with this method (using an HLA type to target) is that if you're targeting MHC Class II, it's going to be hard to kill the victim quickly.  Kill off all the cells would give a person AIDS, but not necessarily lead to a quick death.  Targeting MHC Class I could get around this, but then you're not targeting specific cells (could be nerves, could be skin cells), and the person would probably mount a pretty good immune response.  You'd probably have to hit the person with a pretty high dose to be sure you were infecting the cells you wanted to kill.
If you're willing to allow a two-step process, I think the more targeted approach would be to create an inducible latent virus.  Take one that commonly infects humans like CMV, and modify it so that it was only induced out of latent infection by a specific trigger (tagged food for example).  Then further modify it so that it generates a highly toxic protein when it comes out of latency, like botulinum, that will both kill the person very quickly and have the possible appearance of something natural.  If you use food is a trigger, then health workers would eventually figure out were all these people were eating and accuse them of food poising with botulism.  Whether that can help your character in the plot, I don't know.
Back to the creation of the virus, I would still use the method above, though it's important to note that botulinum is a select agent, and that proper BSL would be a serious concern.  Have a hard time imagining it going down in someone's garage without them killing themselves.  But if the person known how/has materials for gene synthesis (many, many labs do), then acquisition is just a question of making the gene for the published botulinum sequence.
It does occur to me that I might not should even post this based on it's ability to work...feel free to vote/comment to close if that is conciseness.

I would pick some virus that infects all people but then engineer it to not work properly on some specific host cells, e.g. some allele somehow preventing transcription of some key viral protein sort of like RNAi..


text:
Species of this White Dove
I visited a bird enclosure close to where I live in Australia. The enclosure had several different species. The birds that stood out most were these doves sitting right along the fence railing, making a deep "Wo-wo-wo-woo" sound. That and also I thought they looked and sounded similar to Spotted Doves.

Does anyone know what the species of this birds may be?

if you still have any doubts or need any sort of clarification feel free to comment

I think this is a Barbary dove (or Ringneck dove). See this image (from the here):

More information can be found here and here. The second pages shows also images of different color variations.

I accepted @agha rehan abbas before, but only because I didn't see your answer. The Barbary Dove seems to have a white and brown wing tip, while the Collared Dove has solid colour for it's wingtip. The one I saw has the same type of pattern on it's wingtip.

it is symi bird and more over it is commonly called as collared dove its a resident of symi and would have brought to australia by other means

you can find a list off all the symi birds here


text:
What equipment would one use to modify a virus?
Would anyone be so kind as to give me a few examples of the equipment involved when modifying a virus? Otherwise my novel may end up reading
Eva entered the lab and modified a virus.
Not much back story there!

Even though you actually intend to get the facts right for your story, it is better to ask it as a biology question. It would be great if you can edit the question to sound so. Otherwise this question is tending to be off-topic.

To help you frame a better question I can give you this hint- To modify a virus, you have to modify its genome (DNA or RNA in some cases) :)

It's not clear the biological purpose for how you want to modify a virus. As WYSIWYG suggests, the genome is one way, but it is also possible to modify a the external capsid of a virus and give it new function (think targeting a virus for chemotherapy).

(I voted to close because it appears to be homework & is too broad)

I actually am an expert at this, and I have always wanted someone to use forward genetics in a well researched piece of fiction for what it's worth.  Feel free to try and ask more targeted questions, and I'd be happy to answer.  I would also like to point out that considerable amounts of time and failure are to be expected.  Even on a proven recombinant system I would put 1 month minimum to recover, purify, titer, and sequence a new virus.

I'm no expert at this and I would welcome any changes to this post. First you need to decide, what your target organism which you want to infect is (e.g. mammalian cells, bacterial cells) and based on that you choose your viral vector as listed in this article. Generally for mammalian cell stable transfection (usually you want the genetic materials you introduced to persist between cell divisions hence stable transfection) and transformation (just a general statement about changing cells as you have introduced, usually foreign genetic material but transformation is not necessarily the same as making something immortalised, which means the cells won't stop dividing i.e. becoming cell lines or in lay term cancerous) scientists tend to use lentiviruses, which are retroviruses, similar to HIV and they can even infect non dividing cells (so this should allow your imagination to run wild!). Once you have decided what the best viral vehicle for targeting your cells of interest is then you essentially transfect the plasmid DNA (packaging vector), which produces the virus protein package, into cells, whose job becomes to produce the virus as those cells have the required cellular machinery for this purpose. These cells are often 293T packaging cells. Along with the plasmid (circular) DNA, which produces the virus package, you co-transfect the packaging (e.g. 293T) cells with another plasmid, called lenti-vector, which does whatever you want it do, such as express a particular protein or microRNA or whatever but the idea is that stuff produces by the lenti-vector should not be toxic to the target cell (i.e. the cells you intend to target), unless thats what you want it to do.
Now as you can see, you can play around with two things here, first the packaging vector, to change the behaviour of the virus if you wish. And second the lenti-virus vector, to produce whatever you want it to! Once the packaging cells made your viruses, containing your lenti-vector, the virus get secreted into the media, which the packaging cells are in so you have to extract the media, congaing the virus, and concentrate the virus using centrifugation. Once you got the virus then you can use it to transform the (target) cells you wish.
For the lab based procedure of how you make the virus and what equipments you use and how to concentrate the virus then please see this link, although its a little technical. In this case, the packaging vector is fuGENE 6 and the lenti-vector or just plasmids of interests are listed (please not that I do not endorse any products mentioned here and I'm just using it as an example).
Now for making the packaging plasmid (making the virus), you often use the genetic materials from a virus and change it through a procedure called polymerase chain reaction (PCR). Same goes for the lenti-vector/plasmid as they are derived from somewhere and then change through time using PCR and restriction digests, which is an equivalent of genetic material cut and paste, to make the vectors and products of interest. Once all is done the the virus can infect the target cells and effect it based on its designed function (defined by the two vectors I described).
If the above response does not answer you question, since it is currently very broad, please make further clarification to the question so that I can modify my response accordingly.

Consider this as a summary of the previous answers. Also, I am elaborating more on how to make self-sustaining mutated viruses
Points to consider before you think about working with viruses:-

Viruses are pathogenic and the biologist working on them faces a risk of infection. Viral work is always carried out in a protected environment at high biosafety levels.
Viruses need a host to survive. You need to culture host cells or use a live organism to propagate the virus. Generally one goes for the latter only if cell culture methods are unfeasible.
Almost all viruses have a very small genome (which can be replicated very fast), that can be either DNA or RNA. The genome has only very few essential genes that are responsible for the virus capsid (external shell) formation and early replication; most other factors required for the propagation are hijacked from the host.

Having identified and obtained a suitable host, one can proceed to genetic manipulation. The lentiviral vectors that Bez described are basically partial viruses. One part codes for the capsid and cannot make active viruses by itself whereas the other holds the genes for replicative function. So in a way the lentiviral vectors are disarmed viruses that are used as molecular biology tools. But what you are looking for is different.
To modify a virus you need to make mutations in its genome. Once you have identified what mutations are to be made then as previously mentioned, PCR can be used to incorporate them. This technique is slightly different from a usual PCR (not in principle, though) and is called site-directed mutagenesis. For ease it is always better to clone (fix) the viral genome in a plasmid (circular DNA that can be propagated in a usual lab bacteria- E.Coli). After mutating the viral genome, you can excise it from the plasmid. Note that PCR is done with DNA. For RNA viruses you need to convert its genome into a DNA sequence before you go for site-directed mutagenesis. Conventional technique would be to reverse-transcribe the viral RNA. But nowadays chemical DNA synthesis has become quite easy and you can synthesize entire viral genome in a "test-tube".
Having done this, we proceed to the trickiest part: How to get this genome to form an active virus?
Some viruses, as mentioned before use RNA as their genome (poliovirus, retroviruses, common-cold virus etc) while some use DNA (chickenpox, smallpox, herpes etc). The mutagenesis, however, is performed on the DNA. For DNA viruses, introduction of the viral DNA into the host cell, using the conventional transfection methods, might work. For certain RNA viruses like poliovirus this DNA has to be transcribed to RNA. This can be done using a technique called in-vitro transcription (IVT) and the RNA product can be introduced inside the cell. IVT wont work well for long RNAs. In such cases you can use the cell itself to make the RNA instead of doing it in-vitro. Use a plasmid that can transcribe a DNA sequence inside a host cell- this is fairly common and almost all molecular bio labs will have such plasmids. Transfect this plasmid inside the host cell and it will make viral RNA, which in-turn will make active viruses.
Retroviruses work slightly different from other RNA viruses. They have an RNA genome that they convert to a DNA. This DNA gets integrated in the host genome and keeps producing viruses. To make a retroviral DNA integrate you need an enzyme encoded in the virus- integrase. You can clone integrase separately and co-transfect it with the viral genomic DNA.
A couple of final points to consider:

Some viruses such as retroviruses can mutate very fast naturally, because of their error prone replication. They may lose the incorporated mutation unless the mutation provides them a tactical advantage (this is true for all organisms).
I share with many others this opinion that that bioterrorism should not be glamorized. So take care to present it well :)

I would not start from so bottom as Bez in making viruses.
This is very very long project.
It is much less cumbersome task to consider modifying virus, since it already occurs passively in real life.
I would choose equipment based on the characteristics of the virus.
I would start to develop equipment needed for the specific project, since there is no ready solution for this kind of task.
The equipment can be targeted to

actively changing virus (ss(-) and ss(+) RNA virus)
virus not changing so much (here you have to think how you ignite the point mutation and why).

I would use iPS stem cells to as an target but to get this far is very very long process still.
I would focus on antigen presentation - again very many fine regulation factors in Interferons etc should be considered in the special viral case - note that the interferon research is now in an active phase but early.
Interferons are specific so specific parts of the equipment should exists to detect them - for instance, IFN-gamma.
Viruses are generally extremely difficult to control - shortly existing in one form.
You can imagine how difficult they become after editing them real life.
So the plan would be first to understand some easy virus and its early stages in the replication.
You can actually choose a virus that undergoes continuously point mutations (drift mutation) like influenza virus.
However, I would pick something that is not so changing (not RNA virus).
There is no good equipment to do regular analysis of the changes in the influenza virus.
It always requires much work to recognize which genome part has changed and how much internationally.
The vaccines are made based on reports from many countries about their influenza virus statuses and their genomes.
Some simple DNA virus with very slow but fixed point mutations in time so you have time to research them and you can estimate when the next change is going to be.
It would be also useful if you know which part of the virus is going to change (particular plasmid).
This makes the research much more manageable.
Sufficient time-series analysis and group of Mathematicians are also needed to understand different data from different stages.
Actually, your task is extremely broad.


text:
how can a pseudo coelomate like ascaris lay 200k eggs in a single day
as per this site the dimensions of eggs of ascaris lumbricoides are 78-105 microns and as it is shown in the pic down here only half of the body cavity would be used for storage of all the stages of different sizes of eggs

and as we all know pseudo coelomates have very minute width of their body cavity
and rest of the body cavity is filled with mesoglea
so my question is how can a round worm accomodate $2$x$10^6$ eggs in its womb before its release

First of all, the statement that "pseudo coelomates have very minute width of their body cavity and rest of the body cavity is filled with mesoglea" is not correct at least for (large) nematodes and priapulids: they have quiet voluminous body cavity and no mesoglea. In small nematodes (to which Ascaris doesn't belong) the body cavity is indeed vestigial, but the "space" between the organs is filled with extracellular matrix.
Another point is that the eggs in nematodes develop not in the body cavity directly, but in the ovaries and uteri (as correctly shown in the picture you provided), which indeed occupy very large part of the body.
Now to the question about the counts: individual capacity of a single female 29 cm long was once (see also) estimated to be ca. 27 mln eggs contained in its ovaries and uteri, which is impressive, but reasonable given the extremely small size of the eggs and extremely large size of the worm.
If we very coarsely approximate the volume occupied by a single egg with a cube 70x70x70 µm3, we get ca. 9 ml for 27 mln of them, and not much imagination is required to see, how a female ascarid can find room for this volume of relatively loosely packed eggs in its genital system.
EDIT:
To check my statement about "quiet voluminous body cavity and no mesoglea" one can open any modern textbook on invertebrates (or attend a practical course of invertebrate zoology). This is how the nemotode body cavity is described in the monograph "Nematoda" by Vladimir Malakhov (the original I cite is in Russian, but there is also a translation of the book):

"The presence of a spacious body cavity is considered to be the most characteristic property of the whole class of nematodes".
"Schizocoel [= primary body cavity] doesn't have its own walls made of cellular material and is represented by spaces between organs filled with liquid".
"Nevertheless, it should be stressed, that the opinion of the schizocoel being a voluminous body cavity, appeared as a result of investigations on large parasitic nematodes."

Please add a reference backing up your statement: 'they have quiet voluminous body cavity and no mesoglea.'

in summary - very small eggs

authors: فيوتشر أكاديمي


text:
What is Mycoplasma Lyo medium?
Used for instance in this article

The role of genital mycoplasmas as pathogens - - are
  generally neglected by diagnostic laboratories in the United Kingdom,
  possibly due to the lack of a suitable commercially-available culture
  medium. We have evaluated the bioMerieux Mycoplasma-Lyo system using
  qualitative and quantitative studies and have found it to have
  suitable qualities and practical advantages for detection of
  Ureaplasma urealyticum and Mycoplasma hominis.

What is Mycoplasma Lyo medium?
I think it is some sort of anaerobic solid medium for all other mycoplasmas except M. pneumoniae (strict aerobe).

i think your guess is right as lyo means a solution [ref:lyophobic-meaning feared of other solution] and more over the site also has column to comment in where you can comment your question and you might get your direct answer over there

Lyo could just mean the medium is lysopholized. I've checked the company that makes this stuff and not found an answer yet

@rhill45 Did you mean "lyophilised" as in freeze-dried? I don't know of "lysophilised" as a term.