What exactly does the phrase "chimerical sharing" mean in this abstract? The Gizmodo article Australian Siblings Are Semi-Identical Twins, Some of the Rarest Humans Ever links to the new paper in NEJM Molecular Support for Heterogonesis Resulting in Sesquizygotic Twinning Gabbett et al. N Engl J Med 2019; 380:842-849 DOI: 10.1056/NEJMoa1701313.
The abstract of this paper says:

Sesquizygotic multiple pregnancy is an exceptional intermediate between monozygotic and dizygotic twinning. We report a monochorionic twin pregnancy with fetal sex discordance. Genotyping of amniotic fluid from each sac showed that the twins were maternally identical but chimerically shared 78% of their paternal genome, which makes them genetically in between monozygotic and dizygotic; they are sesquizygotic. We observed no evidence of sesquizygosis in 968 dizygotic twin pairs whom we screened by means of pangenome single-nucleotide polymorphism genotyping. Data from published repositories also show that sesquizygosis is a rare event. Detailed genotyping implicates chimerism arising at the juncture of zygotic division, termed heterogonesis, as the likely initial step in the causation of sesquizygosis.

There are several terms I am trying to understand here:

sesquizygosis and sesquizygosity: A postulated form of twinship, in which individuals share between 50 and 100% of genetic identity by state (number of shared alleles).
heterogonesis: The assortment of two or more paternal genomes into distinct cell lineages after polyspermic fertilization of an ovum.
juncture of zygotic division (?)
chimerism

So far I understand that the chimerism means for each fetus, some cells have a distinct genome from other cells, and sesquizygosity means (at least) that there is DNA present from more than one sperm.
But I don't understand what "...chimerically shared 78% of their paternal genome..." means exactly when speaking about twins. What does chimerical sharing mean in this case? Are we talking about four genomes (two genomes in each of two fetuses)? If so, how does that comparison reduce to a single value of 78%?

Heterogonesis \ he-tə-rō-gō-ˈnē-səs \
The assortment of two or more paternal genomes into distinct cell lineages after polyspermic fertilization of an ovum.

Visual Representation:

This term — chimerical sharing seems to be used only in this study as a google search did not return any other results. So, it is not a standard term. I believe what they mean by this term is that the twins shared x% of the paternal genome but the sharing is not homogeneous for each cell. In other words each twin has some cells with genetic material from sperm-1 and the others with genetic material from sperm-2.

If the two sperms were genetically identical, then you would not see any chimerism. Let's now consider only one allele as a marker of paternal parentage. So, there will be two populations of cells for each allele.  If both populations are of the same size then you would have 50% chimerism in a single individual (i.e. the allele frequency). The percentage of chimerism may be different between the twins.

Now, there may be several genomic regions at which the paternal-genomes differ. Since the paternal chromosomes would not be symmetrically partitioned between the blastomeres, the different genetic markers (alleles) are likely to have different extents of chimerism.

In this study they measured the frequencies of a few SNPs that were informative for deducing the parentage.

  Analysis of SNPs from twin amniotic fluid and parental blood showed
  that 265,489 maternal and 179,205 paternal SNPs were informative for
  parent of origin.

They noted that ~78% of the paternal SNPs were found in both the twins.

  Of these, the twins shared 265,400 maternal and 139,155 paternal SNPs,
  which makes them 100% maternally identical and 77.7% paternally
  identical.

Note that this is just a qualitative test for the presence or absence of the alleles. This does not say anything about the extent of chimerism of different alleles. (There are some figures in the supplementary data for the frequencies of different SNP but they are not in a tabular form and hence difficult to deduce).


Why doesn't human consumption of plants cause infectious diseases the way consumption of animals can? At first I want to clarify that I do know that there are naturally poisonous plants and plants that can hold radioactive stuff or toxic material from the environment.

What I mean by "diseases" (I guess there is a special term for that in English) is Bovine Spongiform Encephalopathy and similar serious issues caused by eating animals, by that you cannot develop when consuming plants.

As far as I know there are no diseases causes by eating fruit and vegetables (of course, except parasites if you don't wash it properly and an infected cow or bunny pooped on it ;D)

Is it because the parasites and diseases infecting plants are so specialised for their "body-type and genetics" that they cannot operate inside an animal body?

Could somebody explain that to me in more depth why by eating plants you cannot get a disease (except allergic reaction/intolerance or toxicities as mentioned earlier)?

If you mean if there are viruses, pathogenic bacteria or fungi that may cause diseases both in plants and in animals, the response would be that this is very unlikely (But even so, some fungi and bacteria could do it if some circumstances are given). This is due to some key factors:

First of all, the philogenetic distance between plants and animals is huge. Diseases transmitted by the consumption of animals are called zoonosis, and obviously it is more likely to catch a zoonosis by eating pork than eating shrimps or clams. While it's true that certain parasites have different hosts and use them to transmit themselves (for instance, many platyhelmintha uses mollusks or insects to spread themselves towards mammalian or avian hosts) parasites than have only one kind of host usually are adapted to live inside them, and they usually are unable to infect different organisms. Very few parasites can infect a human and a starfish, and even fewer can infect at the same time a human and a tomato plant.

Second, and related to the first, plant physiology differs completely from animal physiology. Plants usually defend themselves by their natural barriers (cuticles, cell walls), hypersensitive response (programmed cell death in order to limit the spread of a pathogen), isolation and/or outgrowing of the pathogen and accumulation of chemicals. Animals main mechanism is immune system. There are very different strategies and very few organisms can effectively avoid all of them at the same time. In the case of viruses, they would even have to face the fact that animals and plants have huge genetic differences.

Third even if they could, the pathogen will face competition against other pathogens that would be more specialized. Bacteria and fungi can be really hostile towards their microfoes, using a wide array of strategies. This hypothetical pathogen would be very unspecific, so they would have a hard time against more focused microbes. It should be noted, however, that unspecialized organisms usually have a great advantage if the environment have some perturbation, and they also are more resilient toward stress. Many plant pathogens are generalistic organisms that attacks when the plant is harmed or stressed. The same applies to many opportunistic infections in animals.

Despite all of this, there are some diseases that should be mentioned. Some fungi of the Clavyceps genera are plan pathogens, but they produce toxins than can affect the nervous system of animals, causing an intoxication called ergotism (the most famous of this chemicals is the lisergic acid, also known as LSD). Other fungi can produce toxins while they grow in plant tissue. Moreover, there are many fungi that can grow both in plant tissue and as animal parasites (mainly arthropods and nematodes), but in this case the plant pathogenesis usually occurs only when high fungal concentration is achieved or the plant is already damaged. While it's not a real infection, plant pathogens can cause allergic reactions. Finally, phytopathogenic fungi and some bacteria can cause infections in wounds or mucoses in individuals with a compromised immune system, but in this case the source seems to be the spores in the air.


Do men have more extreme variations than women? This question was considered unsuitable for Skeptics and I think it is more suited to BIology than Cognitive Sciences

I was reading this article which I found interesting. It is not supported with references but was an invited address for the American Psychological Association.

It makes the claim that men go to more extremes than women.

People can point to plenty of data that the average IQ of adult men is about the same as the average for women. So to suggest that men are smarter than women is wrong. No wonder some women were offended.

  There are more males than females with really low IQs. Indeed, the
  pattern with mental retardation is the same as with genius, namely
  that as you go from mild to medium to extreme, the preponderance of
  males gets bigger.

[...]

  Almost certainly, it is something biological and genetic. And my guess
  is that the greater proportion of men at both extremes of the IQ
  distribution is part of the same pattern.

[...]

  Nature rolls the dice with men more than women. Men go to extremes
  more than women. It’s true not just with IQ but also with other
  things, even height: The male distribution of height is flatter, with
  more really tall and really short men.

Another notable example of a similar claim was Lawrence Summer's speech regarding the possible reasons for dearth of women in tenured positions in science and engineering at top schools.

Summers outlined 3 possible reasons, with a major kerfuffle erupting - resulting in his firing from the job as a Harvard University President - over his presented second reason [ quotes from Wiki ]:

  The second hypothesis, different availability of aptitude at the high end, caused the most controversy. In his discussion of this hypothesis, Summers said that "even small differences in the standard deviation [between genders] will translate into very large differences in the available pool substantially out [from the mean]

  Summers referenced research that implied differences between the standard deviations of males and females in the top 5% of twelfth graders under various tests. He then went on to argue that, if this research were to be accepted, then "whatever the set of attributes... that are precisely defined to correlate with being an aeronautical engineer at MIT or being a chemist at Berkeley... are probably different in their standard deviations as well".

QUESTION: Are there any studies or evidence to support the claim that men have more extreme variations than women (in other words, that the trait's distribution in males have fatter tails) in a variety of traits?

Possible areas of research can be:

Intelligence (general IQ or specific linguistic or spacial abilities)
Physical attributes (strength, height, weight)
personality traits

for lack of anything better, let's take the FFM's Five:
openness
conscientiousness
extroversion
agreeableness
neuroticism

In order for the answer to be "yes", the research needs to show fat tails in at least 5-6 traits from all 3 of the buckets above (intelligence, physical, and personality), although precise trait mix may be arbitrary and not necessarily limited to my examples, as long as 5-6 somewhat independent traits fit.

In order for the answer to be "no", at least 8 of the 11 traits above should have no fatter tails in men.

Anything else means "inconclusive".

First of all for the first 22 chromosomes (and the mitochondrial chromsome) are the same between women and men. The X and the Y together are something like 1.5% of the total DNA in the human cell.  The X chromosome is also in common, so it has the same chromosomal (genetic) variations the same as women and men.

While I am not sure about the differences you point out, its for sure there are lots of differences between the biology of men and women!  The reason that women's traits might have different variances than men comes from the fact that in women there are 2 X chromosomes and in men there is only one, as well as the additional Y chromosome.

If there are any singular defects in the X chromosome a man carries, it will not be balanced out in the human male.  (other organisms have different sex chromosome schemes).  For instance because there is a cluster of genes that help the eye see in color, women's sense of color (i.e. from their cone cells) is sometimes better than men.  With 2 X chromosomes there is even the possibility of a woman who has four different color receptors in their cones.

On the other hand, why men see better in the dark (i.e. greater sensitivity in the rod cells), is possibly due to an extra Blue Rod pigment gene that remains on the Y chromosome (see above reference).  This is both an accident of genetics, but also an adaptive 'choice' that men would have different visual acuities than women.

Its also known that woman and men may have different epigenetic patterns, with some epigenetic modifications coming from the mother and others from the father.  This is adaptive and also not the direct result of the XY chromosomes.

Interestingly, it turns out that for the most part women's 2 X chromosomes are mosaic.  That is, in each cell only one of the randomly selected X chromosomes are active.  Recessive/dominant X genes are often not the case.

This could result in a greater observed genetic variance for women because when you have two chromosomes, often one of the genes is completely silenced.  Women display all of the alleles of their X chromsomes, whereas men have only one X chromosome entirely, the Y chromosome being much smaller.

So in other words, I would say that while men and women actually have the same variation in their DNA sequences, there are different patterns in the X and Y Chromosomes that might create more variance in terms of what we see in women's displayed genetic traits.


DNA replication : binding Regarding an activator, does the C amp cap complex, bind to the coding strand, the template strand, or both?

Both. You should note that activation in this case involves recruitment of RNA polymerase to drive transcription, and that this process is irrelevant to DNA replication. B in the figure shows amino acid contacts (from CAP) with specific nucleotides in the DNA duplex.

DNA binding by CAP: structure of the CAP-DNA complex.

(A) Structure of CAP in complex with its consensus DNA site (PDB 1RUN) [14], showing primary- and secondary-kink sites. CAP is in cyan; DNA and cAMP bound to CAP are in red. The crystallization DNA fragment contained a single-phosphate gap between positions 9 and 10 of each DNA half-site (Fig 1b).

(B) Summary of CAP-DNA interactions. Shaded boxes indicate positions at which CAP exhibits strong sequence preferences [11,15,16,17]. The black circle, black rectangles, and black diamonds indicate, respectively, the two fold-symmetry axis, the primary-kink sites; and the secondary-kink sites. The black vertical lines indicate the positions of single-phosphate gaps present in the crystallization DNA fragment. The cyan ovals and cyan circles indicate, respectively, amino acid-base contacts and amino acid-phosphate contacts.

Figure from:
Catherine L. Lawson, et al. 2004. Catabolite activator protein (CAP): DNA binding and transcription activation. Curr. Opin. Struct. Biol. 14:10.


What are Intersensory Associations? While I was reading about "Neural Control and Coordination" I came across this
"Association areas in the forebrain are responsible for complex functions like intersensory associations, ....."

What are "intersensory associations"? I have searched the net but could not find anything useful.

A more common terminology regarding 'intersensory associations' is multisensory or crossmodal integration. Crossmodal integration takes place in the association cortices in the brain (Fig. 1). An example is the coupling of auditory and visual input during lip reading, as mentioned in the comments. Lip reading can aid in acoustic speech understanding, especially so in the hearing impaired.

The association cortices include most of the cerebral surface of the human brain and are responsible for integrating the sensory input that arrives in the primary sensory cortices. The diverse functions of the association cortices are loosely referred to as “cognition,” which literally means the process by which we come to know the world. Cognition enables us to attend to external stimuli, to identify the significance of stimuli and to plan meaningful responses to them. The association cortices receive and integrate information from a variety of sources and in turn influence a range of cortical and subcortical targets (Purves et al., 2001).

Fig. 1. Association cortices. source: Brown, Physiology & Neuroscience websites

Reference
- Purves et al., Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates; 2001


How far can we go in engineering our own evolution? After recently seeing Christopher Nolan's Interstellar and reading Kip Thorne's The Science of Interstellar, I've seriously been reflecting on the challenges mankind faces in becoming space pioneers, which in my belief will be a necessity to survive as a species. Not just the technological challenges, but the biological ones as well.

Technology can only go so far to aid and protect an organism against the brutal environment of space travel. And so the day may come where we have to make a choice on engineering our own evolution to become a hardier species that can better cope with that environment. The two immediate attributes that come to mind are resistance to radiation and extended life spans.

And this brings me to my question. Putting aside for the time being the question Should we make this choice ?, my question is How far could we go towards engineering a space-durable human species?

How far could we go towards engineering a space-durable human species?

I think this question is likely to get closed as off-topic. It is extremely hypothetical and would be a better fit on WorldBuilding.SE. But here is my messy attempt to answer this question.

Assumptions

So, I guess in your question, you assume that we know everything about how our genotype (≈the genes of an individual) make up the phenotype (≈how we look basically). So, I will try to give a short answer to this question by assuming that we were to know exactly what would happen if we were to add the sequence ATTTAG in the somewhere in the alpha-globulin gene or the sequence CCTATA somewhere in the regulatory sequence of the lactase gene. It is important to understand that today we are very far from having such knowledge. I also assume that we are able to recreate the environments we need to develop the new thing (human2.0 if you want) that we would have engineered. For example if we make up humans that need to grow in a different environment than the womb. By the end of the answer, I will pretty much assume that we know everything that can be known about organic chemistry and how chemicals process genetic information. Note that to the point we're doing the drastic modifications I will be talking about, it will be a philosophical issue to decide whether the new species we created is a human or not (it may even come to the discussion whether the new thing we created is a living thing or not).

Resistant to evolution as a species or only resistance as an individual?

Are talking about a species that would definitely be resistant to survive in these extreme environments or are you talking about a bunch of individuals surviving in this extreme environments. The difference is "evolution". Species evolve and not necessarily in the right way. High radiation may yield to high mutation rate and therefore to mutational meltdown (decrease in mean fecundity of the population through time yielding to extinction of the species).

General Limitation

With these very extreme assumptions, then we are only limited by physics. We could not add wings of the size of the wings of a warbler to a big animal like human and hope that it is going to fly.

Resistance to radiation

I know little about this subject but will try to say some things that may eventually help you. We cannot really make our DNA insensitive to radiation (although we may eventually make our DNA slightly more stable) because radiation will alter matter. It is a physical process that cannot be altered. We may create a lot more of tumour suppressor genes to protect ourselves from developing cancer. Eventually we could create a species that would be able to synthesize (and carry) a concrete shield around its body to protect itself from radiation. But it might eventually be easier to code genetic information with something else than DNA! Eventually made up of quartz because quartz is relatively insensitive to radiation. We could indeed create a whole new form of life.

High radiation yield to high mutation rate and high mutation rate may likely lead a species to extinction (mutational meltdown) but not necessary directly kill the first generations of this made-up species.

Extending lifespan

This sounds "easier". We may "just" target the alleles (=variant of a gene) that are known to diminish the human lifespan, to slightly (but probably considerably) increase human lifespan. Again, I assume that we can know these alleles and can replace them with better variants. However, evolutionary processes will just recreate those genes, just because there always has an equilibrium between the rate at which new deleterious mutations appear and selection purging the genome from these mutations. Moreover, at an age where reproduction has already occurred selection is less important and it allows for deleterious allele that are expressed late in the age of the individual to eventually spread in the population.


What are the principles of stem cell engineering? Suppose you want to convert the skin cell into a pluripotent stem cell. I know there are a few genes that were identified for this purpose (a recent Nobel Prize). But apart from finding such genes, it also seems to involve maintaining the right environment, such that some critical receptor doesn't get triggered and alter the entire expression. It also seem to involve ensuring gene expression stability after the change has occurred. Could someone add to this? What are the broad paradigm ideas in stem cell engineering?

The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation

  Current reprogramming technology, pioneered by Takahashi and Yamanaka
  1, was built on several seminal advances in the field of
  developmental biology. First, nuclear transfer experiments
  demonstrated that a somatic cell nucleus could be epigenetically reset
  to an early developmental state [2]. Second, cell culture conditions
  were developed that allowed for the isolation and culture of
  pluripotent cells, termed embryonic stem (ES) cells, from the inner
  cell mass of the human and mouse blastocyst [3,4]. Finally, study of
  these cells and of early embryonic development led to the
  identification of factors that were ultimately able to reprogram mouse
  embryonic fibroblasts (MEFs) to the iPS cell state when ectopically
  expressed, albeit at low frequency.

  Reprogramming of somatic cells is a multistep process that culminates
  in the expression of pluripotency genes such as Nanog. Although
  morphological changes occur at early and intermediate stages of
  reprogramming, pluripotency gene expression is only induced during the
  late stage and indicates faithful reprogramming.

  The core reprogramming cocktail, consisting of the transcription
  factors Oct4, Sox2 and Klf4 can be augmented by the
  addition of factors that enhance the efficiency of iPS cell
  generation

Its a multistep process in which much research is still needed,

  The frequency with which somatic cells convert to iPS cells is
  typically below 1%. Therefore, much effort has gone into improving
  reprogramming.

specially to increase efficiency of iPS cell generation

  The ability of cells to pass through the cell cycle has also been
  shown to be an important determinant of reprogramming efficiency.
  Knockdown or gene deletion of p53, p21 or proteins expressed from the
  Ink4/Arf locus allows cells undergoing reprogramming to avoid the
  activation of cell cycle checkpoints and cellular senescence, leading
  to greater iPS cell formation [21],24-27].

Gene expression changes during reprogramming


When looking at skulls from early hominids, how do we know their language creation abilities? If there are no vocal chords left, how do scientists deduce what sounds the specimen was able to create?

If there are no vocal chords left

The hyoid bone, which is part of the voice box, does fossilize -- at least occasionally -- and can be used to partially reconstruct the larynx capabilities, so this premise is wrong.

  We now report the discovery of a well-preserved human hyoid bone from Middle Palaeolithic layers of Kebara Cave, Mount Carmel, Israel, dating from about 60,000 years BP. The bone is almost identical in size and shape to the hyoid of present-day populations, suggesting that there has been little or no change in the visceral skeleton (including the hyoid, middle ear ossicles, and inferentially the larynx) during the past 60,000 years of human evolution.

--A Middle Palaeolithic human hyoid bone

  The Dikika australopithecine hyoid body proportions are chimpanzeelike.  ... The Kebara hyoid dimensions (body alone, and articulated body and greater horns) are almost all within the observed range for human hyoids. Discriminant functions clearly distinguish human from African ape hyoids and classify the Kebara 2 hyoid as human  ...  the expanded bulla characteristic of the African ape and australopithecine hyoid body is therefore interpreted as reflecting the presence of such a laryngeal air sac extension. Its absence in the human, Neanderthal, and H. heidelbergensis (Atapuerca SH) hyoids implicates the loss of the laryngeal air sacs as a derived Neanderthal and modern human trait ...

--Comparative Morphology of the Hominin and African Ape Hyoid Bone, a Possible Marker of the Evolution of Speech

  Modelling of the potential acoustic capability of Neanderthal VTs [vocal tracts] was carried out by Lieberman et al. [24,25] based on their three-dimensional reconstruction of the La Chapelle-aux-Saints fossil ... A different approach to Neanderthal VT reconstruction was taken by Boë et al. [41] who maintained that the Neanderthal larynx and hyoid bone sat lower in the VT than in Lieberman's reconstruction ... In this paper, we report a new study of the speech potential of Neanderthals, based on reconstructions of the positions of the hyoid and tongue root

--Articulatory capacity of Neanderthals, a very recent and human-like fossil hominin

  The description of a Neanderthal hyoid from Kebara Cave (Israel) in 1989 fuelled scientific debate on the evolution of speech and complex language. Gross anatomy of the Kebara 2 hyoid differs little from that of modern humans. ... Because internal architecture reflects the loadings to which a bone is routinely subjected, our findings are consistent with a capacity for speech in the Neanderthals.

--Micro-biomechanics of the Kebara 2 hyoid and its implications for speech in Neanderthals.

As well as larynx reconstruction and anatomic evidence, researchers have other lines of evidence about speech capabilities in Neanderthals and other non-modern humans, such as the genetics (especially the gene FOXP2).


Why it seems that principles of chemistry are not being applied in this biochemical process? According to an answer in this question, my concept used below does not apply:

In the non-cyclic photophosphorylation, consider splitting of two water molecules, then 4 e- (electrons) and 4 H+ (protons) are generated in the lumen of the thylakoid. Due to quinone cycle 8 H+ are transferred from stroma to lumen. 4 e- will reduce 2 NADP+ to 2 NADPH, these H+ are taken from stroma so there is a net decrease of 8 + 2 = 10 H+ and a net increase of 4 + 8 = 12 H+ in the lumen. So if we apply principles of chemistry then to attain equilibrium there should be equal number of H+ on both side. Therefore 11 H+ must be transferred from lumen of thylakoid to stroma. Now there is 1 H+ on each side at equilibrium. We know that F0-F1 ATPase will produce 1 ATP for 3 H+ being transferred so in this process 11/3 ATP should produce but in books it is given that all 12 H+ are transported which is violating the principle of chemical equilibrium and produces 12/3=4 ATP.

So I basically want to ask: Why does it seem that in this process the principles of chemistry are violated?

From the link given by @Kendall

Such a gradient can be maintained because the thylakoid membrane is essentially impermeable to protons.

I think this solves your dilemma of 'why not maintaining equilibrium' totally.

The reason for this difference is that the thylakoid membrane is quite permeable to Cl- and Mg2+. The light-induced transfer of H+ into the thylakoid space is accompanied by the transfer of either Cl- in the same direction or Mg2+ (1 Mg2+ per 2 H+) in the opposite direction. Consequently, electrical neutrality is maintained and no membrane potential is generated.

It precisely shows why electrical equilibrium is not disturbed due to pH disturbance.
Finally:

2 H2O + 2 NADP+ + 10 H+stroma => O2 + 2NADPH + 12 H+lumen
12 H+lumen + 4 ADP + 4 Pi => 4 ATP + 12 H+stroma


This Sequence Data (DNA) has very few Methionin-starts. How is that possible? I'm working on my first sequencing related project and I'm trying to find proteins with a specific PFAM ID (PF11999). The project is called "MMETSP", I searched the annotations for that ID, identified signal peptides using SignalP and their target locations with a tool called MultiLoc2 (I was looking for extracellular targets only).

Out of the very few sequences that where left after all this filtering, none of the DNA-bits started with the basepair-code "ATG", for Methionine. How can this be?

I used the shell to calculate that only 1,83% of all the sequences start with ATG.
Any ideas on this?

If anyone stumbles across this question, I found out what the problem was in the end:
contrarily to my assumption that the DNA sequences where all in proper 5'3'-direction, it turned out that we found the exact ORF on the complementary strand in the other direction and who knows where else. Luckily, the MMETSP-Data also featured a /pep directory, in which the needed sequences where found in a clean version.
Thanks for reading and good Luck.


Why perform imputation? Genetics datasets contain measurements for millions of single nucleotide polymorphisms (SNPs). Some (usually small) percentage of these values are of low confidence, and are labeled as missing values. It is common to impute these missing values using statistical relationships within the high-confidence samples as well as relationships mined from public datasets. This makes sense, to get an estimate of what that small percentage of missing data likely is in reality.

Sometimes, analyses are performed that impute up to a much larger number of SNPs - for example, a genotyping platform might measure 2.5 million SNPs, but imputation is performed to get a larger sample of 6 million SNPs. My question is, what value do the extra SNPs that were never even measured have from an analysis point of view? When performing feature selection or predictive analysis, it would seem that the imputed SNPs are really just encoding statistical relationships that are present in the dataset to begin with. What does it mean to find a highly associated or predictive SNP in the imputed set?

In GWAS we are interested in understanding which SNP has a causal influence on a specific phenotype. At the moment large scale studies are carried out by genotyping arrays. For each SNP we put on the array, we measure the alleles present in the patient.

The cost of genotyping obviously depends on how many SNPs we would like to measure. So the problem when designing a genotyping array boils down to: What SNPs do we put on such an array so that we get most information out of it.

To answer that question it is important to realize that SNP alleles are not independent. SNPs that lie in the same haploblock are highly correlated. So measuring one of these SNPs is often sufficient to predict the alleles of other SNPs that are in so called linkage disequilibrium. When designing a genotyping array, we probably do not want to measure all of those highly correlated SNPs, because we gain very little information. Instead may want to measure just few of them and then impute (predict) the alleles of the correlated ones from population study data.

So back to the GWAS analysis. From the SNPs on the designed genotyping array we now predict SNPs that are associated with the phenotype. Say after our statistical analysis we found an associated SNP. But from the design of our array we know that there may be highly correlated SNPs that we did not measure. All of them will also be statistically associated. If we do not impute, we may come to the wrong conclusion that we already found the true causal SNP. In fact, there may be many and finding the correct is often very difficult.


Are casein proteins in UHT milk digestable for infants or toddlers? As a novice cheesemaker, I have read that Ultra High Temperature prosessed milk is unsuitable for cheesemaking, as casein proteins are denatured and cannot be curdled with rennet.
I have verified that claim experimentally. Although curd has formed, its quality was poor (I managed to make whey-like cheese after further heating though).

As casein is the majority of milk protein and curdling with rennet is important component of milk digestion, I started to worry if feeding UHT milk to toddlers is a good idea. (I also wonder, whether boiling milk may lead to a similar casein denaturation.)

Unfortunately, Wikipedia addresses only the cheesemaking aspect of UHT processing. I do not know whether it is possible to digest temperature-denatured casein (without proper curdling).
Moreover, after some more research I am not sure what is mechanism of milk digestion in infants: Which enzyme curdles milk in human infants?

UHT treatment increases the digestibility of casein.

Ultra High Temperature Treatment, but Not Pasteurization, Affects the Postprandial Kinetics of Milk Proteins in Humans (Journal of Nutrition)

  Moreover, the UHT treatment of milk causes structural changes in its
  protein system. The main change is the denaturation of whey proteins
  and their interaction with casein micelles. Consequently, it was
  expected that the behavior of the UHT milk would be similar to that of
  casein micelles, as observed with native casein. However, it has been
  shown that the interaction between casein micelles and whey proteins
  is also accompanied by a large increase in number of very small,
  soluble particles resulting from the desegregation of casein micelles.
  Consequently, by weakening the interaction forces between caseins,
  heat treatment provokes both a loss of the micelle framework and the
  formation of small aggregates. Correlatively, an increase in the
  amount of nonsedimentable casein has been observed in UHT milk
  following high-speed centrifugation (33). Two effects of these changes
  on milk properties may be softer coagulation and a higher
  susceptibility to enzymatic hydrolysis due to loosening of the
  micellar structure and the presence of small aggregates that may be
  more accessible to enzymes.

In the stomach of adult or infant, gastric acid and the enzyme pepsin denaturate whey and casein proteins from either raw or heated milk Critical Reviews in Food Science and Nutrition). The denatured proteins are then nearly completely digested by the enzymes pepsin in the stomach and by trypsin, chymotrypsin and peptidases in the small intestine (Medical Libretexts.

Humans, including infants do not have the enzyme rennin (chymosin).

  Rennin, also called chymosin, protein-digesting enzyme that curdles milk by transforming caseinogen into insoluble casein; it is
  found only in the fourth stomach of cud-chewing animals, such as cows.
  Its action extends the period in which milk is retained in the stomach
  of the young animal. In animals that lack rennin, milk is coagulated
  by the action of pepsin as is the case in humans. A commercial form of
  rennin, rennet, is used in manufacturing cheese and preparing
  junket (Britannica).

  Chymosin is secreted in the neonatal stomach of ruminants (cattle,
  goats, camels), pigs, cats, and rats. Animals including humans,
  chimps, and horses have inactivating mutations in their chymosin gene
  and do not secrete the enzyme (vivo.colostate.edu).

There's one study that mentions the presence of chymosin in humans, but the evidence seems to be very weak as described in another Biology SE answer. Some articles, like this one mention chymosin in humans without proper references.


Are the IRV and ERV equal in amount? I am reading about Inspiratory Reserve Volume and Expiratory Reserve Volume in my textbook. So my general question is aren't the two terms show the same amount of air ?
I would like to tell you why I think so. Like IRV tells us about the maximum amount of air we can intake other than normal intake. So this extra amount is what going inside our lungs and I think this is the part which comes out in the form of ERV .
So shouldn't the total capacity of lungs be equal to (Tidal volume + IRV + Reserved Volume) only ? Why do we need to include the term ERV in the above equation ?

You're misunderstanding a bit. Here are some definitions from Wikipedia, where I added some bold for emphasis:

Expiratory reserve volume: the maximal volume of air that can be
exhaled from the end-expiratory position

Inspiratory reserve volume: the maximal volume that can be inhaled
from the end-inspiratory level

In plain terms, ERV is how much you can still breathe out after you've breathed out all you normally would. You can try it out yourself: when you're finished breathing out and ready to start breathing in, try to blow out a bit, you'll find there is still air there. You don't need to breathe in extra to be able to breathe out this extra.
Similarly, IRV is how much you can still breathe in after you've breathed in all you normally would.
If you were to do a "fullest possible breath" that would include inspiring as much extra as possible, plus the normal breath volume, plus exhaling the last little bit you can:
IRV + Tidal Volume + ERV
There's still a little bit of residual air left over (RV), though, so:
IRV + Tidal Volume + ERV + RV
gives you the total capacity.


Is there a superterm combining "animal line" and "cell line" in disease models? Biologists researching diseases will frequently use animal models. The way I understand it, there are species of animals, such as "mouse", and lines of mice, such as Black six, NMRI or also genetically engineered lines like B6.Cg-Tg(CAG-cre/Esr1*)5Amc/J. But they also sometimes take cell lines such as HeLa and transplant them into animals, or treat them in vitro.

Is there a word which covers both "animal line" and "cell line" and is in widespread use? I thought that "model organism" would be a good way to express it, but a biologist working in disease models told me that when she hears that, she only thinks of animals, never of cell lines. She wasn't able to come up with a term which covers both. Her best try was "experimental system", but she conceded that, if used out of context, no biologist would recognize that it is about animal and cell lines.

There is no super-term that I can think of but you could say genetically modified (mouse) samples/specimens?


Can catecholamines degrade back into tyrosine, or, is synthesis irreversible? (in human body) Catecholamines like dopamine, noradrenaline and adrenaline are broken down with enzymes that catalyze the reaction. Can they degrade back into tyrosine (a conditionally essential amino acid), or is the synthesis of catecholamines like adrenaline irreversible? (in context human body, but, broadest possible phylogenetic or biochemical context welcome in answer.. )

A glance at the relevant BioCyc entry tells us that each reaction in the catecholamine biosynthesis pathway is irreversible. The standard free energy change of each reaction—again from BioCyc—is given below.

\begin{array} {|r|r|}
\hline
\text{Reaction} & \Delta _r G' ^{\circ} \text{ in kcal mol}^{-1}\\
\hline
\text{Tyrosine hydroxylation} & -93.0 \\
\hline
\text{Decarboxylation of DOPA} & -3.09
\\
\hline
\text{Hydroxylation of dopamine} & -67.9
\\
\hline
\text{Norepinephrine to epinephrine} & -10.5
\\
\hline
\end{array}

Note that all the free energy changes are negative, i.e. all reactions are irreversible under physiologic circumstances. (For the last one, there is a simple explanation: S–adenosylmethionine is a powerful methylator [1].)

Another aspect is worth a mention. Under physiologic conditions, the reversibility of a reaction depends not only on the free energy changes involved, but also on what happens to the reactants and products. A large supply of reactants, or rapid removal of reaction products, can make the reaction physiologically irreversible. Applying this principle to the catecholamine biosynthesis pathway:

A steady supply of oxygen is available from the atmosphere—this drives the tyrosine and dopamine hydroxylation reactions in the forward direction.
The dihydrobiopterin produced by tyrosine hydroxylase is scavenged by reduction to tetrahydrobiopterin, which further takes part in the tyrosine hydroxylase reaction [1].
The carbon dioxide produced by DOPA decarboxylase is exhaled out.

This further adds to irreversibility.

Of course, as mentioned by @user1136 in the comments, it is theoretically possible to have a "reverse" pathway by coupling to ATP hydrolysis. However, I could not find any such pathway in database searches.

Summary: To the best of my knowledge, humans cannot convert catecholamines back to tyrosine.

Reference

Nelson DL, Cox MM. Lehninger principles of biochemistry. 6th ed. New York: WH Freeman and Company; c2013. Chapter 18, Amino acid oxidation and the production of urea; p 695–730.


Is there nothing such as NADPH2? I have gone through various sites and some say there is NADPH2 and some say there is no NADPH2 there's only NADP+ ...WHich is the correct view....Please dont mark this answer as duplicates since I have asked a similar question related to photosynthesis in the past but there too I have not received any satisfactory answer bythe community .

I answered this implicitly in a comment to my answer to: Light and Dark Reaction of photosynthesis?. Anyway:

There is no such thing as NADPH2. There is only NADP+ and NADPH. Consult Wikipedia or a reputable text such as Berg.

The nicotinamide portion of NADP that  undergoes oxidation and reduction is exactly the same as in NAD. The changes undergone are:

The error either comes from confusion with the other redox cofactor, FAD / FADH2, or the fact that two electrons are involved in the reduction of NADP:

  NADP+ + H+ + 2e → NADPH


Rh factor and dominance of gene "Formation of Rh  antigen is controlled by dominant gene(R) and its
  absence by recipient gene(r).People having this antigen with genotype
  (RR or Rr) are called Rh positive and those whose blood is devoid of
  it with genotype (rr) are called Rh negative. About 85% in world are
  Europe and 97% human being in India are Rh positive."

My questions are:-

Which factors result into dominance of gene(R) and  absence of recipient gene(r)?

With difference seen in %ratio in India and Europe, can it be concluded that environmental factors affects it.?

There are various factors which decide the dominance of one gene over the other. Owing to the complex biochemical pathways it is difficult to predict which gene is dominant unless we know exactly how the gene is translated to protein and how the protein interacts with the body.
These are the few answers that could help:-

What makes a gene dominant or recessive
What determines if an allele is dominant or recessive?

As for your question;

There are two genes:

D- The allele which is dominant
d-The allele which is recessive.

A recessive gene is a gene that is nonfunctional or expresses its characteristic phenotype in presence of an identical allele.

For a person to have Rh negative blood group he must inherit 'd' allele from both the parents as it is a recessive trait.And as @swbarnes2 mentioned in the comments 'd' allele is more common in European countries leading to a wide range of population possessing Rh negative blood groups.


High frequency human genetic oscillators? The most well studied genetic oscillators in human genomes are involved in regulating the circadian clock (which operates on an approximately 24-hour cycle) and cell cycle activity (with single cycles usually lasting several hours to many days). Are there any known genetic oscillators in humans (or other mammals) that operate on shorter timescales?

Here are some examples:

electric oscillators:

neural activity
cardiac automatism (0.8 ... 1 Hz)

mechanical oscillators (as a result of neural activity):

heart beats
breathing (0.2 ... 0.3 Hz)
intestinal peristaltic waves
vocal chords activity (up to a few kHz)
muscular spasm (pathological)

chemical oscillators:

insulin variation in concordance with glucose intake
endocrine oscillations
menstruation
feedback enabled metabolic pathways

See this Wikipedia page too: http://en.wikipedia.org/wiki/Oscillation#Human

When it comes to genetic oscillators, some of them follow circadian rhythm.

  A typical proliferating human cell divides on average every 24 h. This division timing allows cells to synchronize with other physiological processes and with the environment. The circadian clock, which orchestrates daily rhythms, directly regulates the cell division cycle and is a major synchronizing factor [5].

Immune system:

  In every single cell an oscillator goes ticking through a molecular clock operated by transcriptional/translational feedback loops driven by the rhythmic expression of circadian genes. This clock gene machinery steers daily oscillations in the regulation of immune cell activity, driving the periodicity in immune system function [1].

Glucose homeostasis:

  The master circadian clock, localized in suprachiasmatic nucleus (SCN), regulates multiple metabolic pathways, while feeding behavior and metabolite availability can in turn regulate the circadian clock [2].

Retina:

  ... the retina itself possesses intrinsic circadian oscillations, exemplified by diurnal fluctuations in visual sensitivity, neurotransmitter levels, and outer segment turnover rates. Recently, it has been noted that both central and peripheral oscillators share a molecular clock consisting of an endogenous, circadian-driven, transcription-translation feedback loop that cycles with a periodicity of approximately 24 hours [3].

But there are others which don't.

  Genetic oscillators are ubiquitous regulatory motifs in the molecular control circuits of living cells. Prominent examples include the cell cycle and cellular signaling [4].

The frequency is much lower in some human cells [6]:

Cell Type      Process    Time
______________ __________ ______________________
fly embryo     mitosis    8 minutes
bacteria       mitosis    20 minutes
yeast          mitosis    2 hours
human skin     mitosis    20 - 24 hours
human sperm    meiosis    about 64 days
human liver    mitosis    1 year or more
human egg      meiosis    up to 40 years or more
human nerve    mitosis    never, once mature

References:

Vinciguerra M, Borghesan M, Pazienza V, Piepoli A, Palmieri O, Tarquini R, Tevy MF, De Cata A, Mazzoccoli G. The transcriptional regulators, the immune system and the the circadian clock. J. Biol. Regul. Homeost. Agents. 2013;27(1):9-22. PubMed PMID: 23489683.
Chrościcki P, Usarek M, Bryla J. [The role of biological clock in glucose homeostasis]. Postepy Hig Med Dosw (Online). 2013 Jun 20;67:569-83. doi: 10.5604/17322693.1053906. PubMed PMID: 23799401.
Ramsey DJ, Ramsey KM, Vavvas DG. Genetic advances in ophthalmology: the role of melanopsin-expressing, intrinsically photosensitive retinal ganglion cells in the circadian organization of the visual system. Semin Ophthalmol. 2013 Sep 6;28(5-6):406-21. doi: 10.3109/08820538.2013.825294. PubMed PMID: 24010846.
Davit A. Potoyan and Peter G. Wolynes. On the dephasing of genetic oscillators. PNAS 2014 ; published ahead of print January 27, 2014, doi:10.1073/pnas.1323433111
Samuel Bernard and Hanspeter Herzel. Why Do Cells Cycle with a 24 Hour Period? Genome Informatics 17(1): 72{79 (2006).
wiseGEEK.org. How Long Does it Take for Cells to Divide? (accessed 21.07.2014)


Can anyone explain the idea of anodic nerve stimulation? Nerves get stimulated under the cathode, according to the conventional current direction. But in some research, it is said that anodic stimulation or anodic current stimulation can activate neurons. How does it occur physically? The picture below shows the two types of stimulation, but I can't get it.

Short answer
Both anodic and cathodic current pulses can evoke neural activity, as shown in your image.

Background
You have to be aware that the current direction is arbitrary and the 'convention' you mention depends on your discipline. In electrophysiology, the anode is generally considered to be the positive electrode, the cathode is generally the negative electrode and the anode the positive. In physics however, current is assumed to be positive (due to historical reasons) and therefore the definition of anode and cathode is opposite.

Secondly, there is no reason to assume that nerves under the cathode are stimulated (and not under the anode), as is shown in your picture - in both cases a neural response is elicited. For example in cochlear implants, biphasic current pulses are used, because these are safer than simple anodic or cathodic pulses. Biphasic pulses are charge balanced and consist of an anodic phase and an opposite cathodic phase. (Cochlear implants are arrays of electroides implanted in the inner ear that stimulate the auditory nerve directly and are used to treat sensorineural deafness).

In animals and humans, both anodic and cathodic pulses can evoke neural responses. In human cochlear implant users, the anodic phase is more effective than the cathodic phase. In contrast, in animals usually the opposite is observed. The reason for this discrepancy is unclear (Machery & Cazals, 2016).

Whatever the exact reason of their differing effectivity in evoking neural activation - both anodic and cathodic current pulses can evoke neural activity.

Reference
- Machery & Cazals, Adv Exp Med Biol (2016); 894:133-42


Overlapping genetic information in eukaryotes In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do remember seeing quite a bit of variation in the direction of the overlapping genes (same vs different directions), the amount of overlap, and even the number of overlapping genes.

I know enough about gene prediction to take any computational predictions with a grain of salt--even those supported by transcript and peptide alignments. However, these cases have me thinking--does overlap of genetic information really occur in eukaryotes? I seem to remember learning (or hearing anecdotally) that it can happen in prokaryotes, and that seems to be understandable given the compactness of prokaryotic genomes. But can this happen in eukaryotes? Has this been studied, and are there cases that have been confirmed experimentally?

You might be interested in the INK4A locus (chromosome 9p), encoding both p19 and p16 genes, very close to p15. You can read a description here. All three proteins are known experimentally to exist.

Now, whether these are two different genes or the same gene with alternative splicing and start sites leading to different reading frames it's up to discussion. The point is that p19 and p16 share DNA coding sequence but not protein sequence nor function.


Scoring sequence against position weight matrix I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability

If I have a sequence say "AAPGTGASMHSGLLW" how would I score it against the matrix? I tried taking the product of probabilities corresponding to the matrix, but I end up with a really small number

Any ideas?

Edit:

Consider the simple matrix:

    1    2   3     4
A 0.3 0.90 0.5 0.0001
B 0.2 0.05 0.4 0.2
C 0.5 0.05 0.1 0.8

The best match is, with a score of:

CAAC = 0.5 * 0.9 * 0.5 * 0.8 = 0.18

If you change the first letter to an B instead of C

you get a match, with a score of:

BAAC = 0.2 * 0.9 * 0.5 * 0.8 = 0.072

Which is a huge difference for such a small change...
This is even worse with my larger matrix since the score is easily affected by small probabilities

The probabilities are correct. You must take the product (in log space this is equivalent to sum). The reason the probability looks small is just that you are perhaps thinking the score should be close to 1. However, this is not the case. To get a score of 1, you need the PWM to have 1/0/0/0 at all positions and get a perfect match.

So what should you compare to? What people usually do is compare this to a background distribution, the easiest being uniform, so the PWM is 0.25 everywhere. For your example, the score in this case will be 0.25^4 = ~0.004 and this is what you should expect by random.

This is why people usually look at the ratio between the score of the PWM relative to the score for the background model (and usually take the log2 of that), which in your case will be 0.18/0.004 = ~46 so the sequence you got is 46 times more than you would expect by random! And for your second example, 0.072/0.004 = ~18 times more than expected, so that is still high.

More conceptually, what you are doing is comparing two probabilistic models, your PWM and a background PWM, and comparing the probability to get your observed sequence according to each one of them. This is a common approach in general for comparing probabilistic models, even if they are more complicated.


Reason for name "Motile sperm domain-containing protein 2" if it has nothing to do with sperm I am interested in a gene with the name "motile sperm domain-containing protein 2".

The entry for the human gene in uniprot suggests that it does not have any relation to sperm or spermatogenesis.

If this is so, why does the name make reference to sperm?

As you can tell from the gene name, it contains a domain (a "major sperm protein domain)") that happens to have "sperm" in its name. That doesn't mean that the protein itself have anything to do with sperm. There are a lot of examples of gene names like this, where they're named after some random domain they contain until later their names are changed. MSOPD2 has only had a known function for a few months.

As an aside, if you actually work on this gene then one would hope that you would have taken the whopping 5 minutes required to figure this out in pubmed.


are sperms considered living recently i got into a debate with this question on hinduism.se ,

as the link given above shows, are sperms considered as living or non-living

as far as my knowledge is concerned, sperms undergo locomotion, senescence, more over the best thing to say they are living is they contain genome, i.e. haploid sets of chromosomes

so in short are sperms living or non-living

The question of what is living is nothing but a matter of definition. We can only tell you what are the standard definitions of what is a living thing but no absolute truth exist behind these definitions. Therefore, I am afraid that all discussions here will bring anything new to your ethic or religion related discussion.

I want to argue that the @user137's answer is very misleading for two reasons. First, he based his discussion exclusively on the "reproduction ability" definition of life. Second because his definition of reproduction might be misleading as well.

Reproduction is not only cell division obviously. Following this same definition one would not consider a human to be a living things but only to be a collection of living (and non-living) things. It is important to understand that a spermatozoid is just one phase of a life-cycle. This phase yield to the next phase. That's it. It seems weird to say that a kid is not alive just because he cannot reproduce. It seems weird to say that a grandmother is not alive because it cannot reproduce. You can say however that a kid is a living thing that cannot reproduce and at another moment of its life cycle it will be able to reproduce (assuming it will survive to this age). One should not think of spermatozoids as something totally detached from the human phase as we know it. These things just form a cycle and it seems to me miseleading to say that a part of this cycle is not alive. Saying such thing would yield someone to think that two living things create non-living things that by fusion will become alive. That seems weird. But again, it is nothing but a matter of definition. I cannot say that user137 is wrong, I cannot only say that his definition seem neither useful, intuitive nor common among biologists.

You may want to have a look to life-cycle and to understand what are the haplontic and diplontic phases with a bunch of wikipedia readings.

Other concepts such as the ability to synthesize its own components, having a boundary between interior and exterior and ability to response to environmental stimulis are often used in order to define what is a living thing and what is not.


Can I simulate a previous and next sequence of my fasta files? I have fasta sequences of a virus protein that had suffered a mutation in 2008 and this mutant had increase it fitness when compared to wild strain (according to literature).I want to simulate if my sequences were submitted in 2009(I have sequences from 2009 and 2010) or before to mutation and simulate next sequences to verify if the population of mutants really turns majority.
How can I do that?My virus is a RNA -ss. Any tool to use that i can represent it graphically?
Or simplifying..I want to simulate the past and the future sequences of my dataset.

From the description of the model you are interested in, you probably don't need numerical simulations. A simple analytical expectation might be enough. But anyway, if you want to perform numerical simulations (maybe you don't want to assume panmixia), then there are a number of choices to you.

The simulator that you will need needs to be able to implement selection. It hence need to be a forward-in-time simulator and not a coalescent simulator. I personally have experienced with 4 different forward-in-time simulators; SimBit, SLiM, SFS_code and Nemo.

If I am not mistaken, SFS_code won't be able to simulate haploid individuals and will probably be slower than SimBit and SLiM. In SimBit, SLiM and Nemo you cannot do haploid either, however, you can set the cloning rate to 100%, which will essentially be the same as simulating haploids.

To my experience and generally speaking, SLiM and SimBit are faster than Nemo. Because your mutation rate is high and because your recombination rate will be very low (will probably be zero), SimBit should be very very fast and SLiM relatively slow. Also, SimBit will offer much nicer outputs for the statistic you are interested in than SLiM does.

Please note that I am the author of SimBit and I therefore might have a conflict of interest here. Here is the link to SimBit.


Is bacillus strain 2-9-3 really 250 million year old? I've read that in the last decade (I believe) some scientists discovered a microorganism, which they dubbed bacillus strain 2-9-3, in a crystal of salt that they think is 250 million years old and that started replicating when put in favorable conditions.

Is this really an example of the longest surviving life form?

Could someone confirm this is true and scientifically validated and provide some info and references that can be understood by non specialists. I'm a telecommunications engineer so I can understand general scientific approach and I have a basic understanding of chemistry and biology, but no formal or specific training on the subject.

Disclaimer

I was unaware of 2-9-3, but performed a simple internet search which brought up a an open-access paper from 2001 refuting the claim, and nothing more recent, suggesting that the refutation was valid. I mention this both to make it clear that although, like the poster, I am not an expert in the topic one can get considerable mileage through standard search techniques. (I do acknowledge that it does help if you know you can get access to papers through a University Library, open-access or not.)

Refutation

The claim was actually made nearly two decades ago in a paper by Vreeland et al. in Nature 407, 897-900. The date is relevant because at that time full-length sequences of bacterial genomes were only just appearing.

The paper refuting the claim is entitled “The Permium Bacterium that Isn’t” by D.Graur and T.Pupko and was published in the journal, Molecular Biology and Evolution 18 1143–46 (2001).

The authors put forward various indirect arguments for doubting the claim but they based their refutation on sequence comparison between so-called Bacillus permeans (2-9-3) and other bacteria. The first argument was that the 99% similarity of B. permeans to a contemporary halophilic bacterium, previously known as Bacillus marismortui, subsequently renamed Salibacillus marismortui, implied a relatively recent divergence from the latter. To rebut the argument that S. marismortui had also been trapped in salt for millions of years until recently a comprehensive comparison with other bacteria was conducted resulting in the phylogenetic tree shown below which was incompatible with the bacterium having not evolved in the last 250 MYr:

An independent analysis by Nickle et al. in Journal of Molecular Evolution 54, 134 (2002) came to a similar conclusion.

I am not expert enough to judge the methods of determining rates of evolution and relative distances between species, but it would appear that they are accepted by those in the field.


Can we digest food as well as herbivores I heard some guy say that we can't digest plant food as well as herbivores. Which seems weird to me seeing as how humans can survive without any nutrient deficiencies besides b12 on only plants but we would pretty much just die of nutrient deficiencies on a carnivore diet. Can someone show me how we can't digest plant food as well as herbivores?

Humans do not have microflora that can hydrolyze cellulose, but plant-eating herbivores do. One advantage of that though is that the cellulose helps move food through your gut and aids digestion. Herbivores have fermentation chambers in their alimentary canals that contain mutualistic bacteria and protists that can break down the cellulose for them; some of the microorganisms also use some of the sugars from the digested cellulose to produce nutrients vital to the animal, such as vitamins and amino acids. Also, herbivores have longer alimentary canals relative to their body size, due to the fact that plant matter is harder to digest because of the cell walls.

Here is an excerpt on herbivore teeth structure, taken from Campbell Biology, 10th Edition.

  "Herbivores, such as horse and deer, usually have premolars and molars with broad ridged surfaces that grind through tough plant material. The incisors and canines are generally modified for biting off pieces of vegetation. In some herbivores, canines are absent" (Reece et al. 906).

References:

  Reece, Urry, Cain, Wasserman, Minorsky, and Jackson. Campbell Biology. 10th ed. N.p.: Pearson, 2014. Print.


Genetic Epistasis Question I need help with this practice question.

I'm assuming that would a epsitatic recessive question since the parents are true breeding and then the ratio would be 9.3.4. But I am not so sure.

Any help would be greatly appreciated thanks!

The Magenta variety is pure breeding, and hence must be homozygous at both loci, (Dominant at Gene A and recessive at Gene B), otherwise, in some of the generation along the family line, there would have been a non-magenta flower, which contradicts the pure breeding nature. But the same cannot be said for the pure breeding white variety, as it can still be homozygous recessive at Gene A and heterozygous at Gene B, it would still exhibit white flowers in all of its progeny after any number of generations.

But the fact that all the progeny of the cross between white and the magenta variety turns out to be red, removes the possibility of the white variety being heterozygous, as that would have produced atleast some magenta plants. Since all were red, we can be certain of the genotype of both the parents, and consequently of the F1 progeny.

This solves your first question. The second question needs the extrapolation of the information gathered while solving the first question into a Punnett square and a simple probability calculation. The third question is a factual question, but it must be mentioned, that this particular type of interaction can be classified under more than one type, and hence a single answer would not be possible for your third question.

ADDENDUM
The third question is actually a bit difficult to answer. The phenotypes will be $\text{A*B*}$=Red, $\text{A*bb}$=Magenta, $\text{aa**}$=white. This gives us $9:3:4$ for Red:Magenta:white. Now the fact that recessive at one locus , Gene A, suppresses the phenotype altogether no matter what the genotype at the other locus, means that one of the phenomenon exhibited is recessive epistasis, where Gene A is the epistatic loci and Gene B is the Hypostatic loci. But, the fact that there are two distinct phenotypes with the epistatic gene dominant, means the interaction is not complementary ($9:7$) but is supplementary ($9:3:4$). This distinction is necessary, and it essentially means that the "intermediate" of the elucidated pathway is also coloured. Otherwise, like in Flower colour in Lathyrus Odoratus, the phenotypes of $\text{aa**}$ and $\text{A*bb}$ are same, and hence the phenotypic ration remains $9:7$. For a ratio of $13:3$ you need domianant epistasis and the phenotypes of double recessive and the epistatic recessive must match. Here, it is recessive epistasis, as the recessive condition at one locus suppresses the expression a other, and not dominant. Feel free to seek further clarifications or simplification.


Why can't we see in low light if staring long enough? For me it seems reasonable that if I kept my gaze on a fixed point in a room with low light, a progressively brighter and better picture would appear before my eyes, just like a camera can see in the dark if the shutter speed is really slow, e.g. 4 seconds exposure. Why can't our brain do this trick as well (accumulate visual information over time)? Or is it a limitation of the eyes?

edit:

To further clarify what I'm after; I will show a concrete example from the world of photography (images taken from this website).

Here is an example where we have a series of underexposed images - this would be what the brain receives:

Now, combining all of them with a simple add-operation reveals one image that has normal exposure.

This seems like a simple trick for our powerful brain - surely it can add incoming signals?

For simplicity's sake, let's really reduce this to something like photography.

A camera's aperture can stay open indefinitely, allowing the plate (or whatever is receiving and recording light) to "collect and save the effect of photons" over time, if you want to phrase it that way. That allows a camera to make images that our eyes never can, for example, of "star trails".

The retina isn't like a photographic plate or a digital sensor's photosites (or pixels). It can't "collect and save" like a camera can. There is a "refresh rate", if you will, that disallows a collection and saving of light that doesn't apply to cameras, because cameras don't care if something in their vicinity is sneaking up on them and presenting a danger to their lives. Not being able to detect change rapidly is something that would be most inconvenient to survival.

  It is the time sampling with long exposures that really makes the magic of digital astrophotography possible. A digital sensor's true power comes from its ability to integrate, or collect, photons over much longer time periods than the eye. This is why we can record details in long exposures that are invisible to the eye, even through a large telescope.

How Digital Cameras Work


Is the affinity of an enzyme or transporter for its substrate or solute influenced by the amino acids at the binding site? The affinity of an enzyme or a protein transporter indicates the strenght of the binding of substrate/solute. An enzyme with higher affinity binds its substrate more strongly than a counterpart with a lower affinity. Is affinity always a function of the protein structure of enzyme? If the same enzyme in two different species had different affinities for substrate, would that indicate that there were differences in amino acids at the binding sites of the enzyme in the two species?

In a reaction which follows a saturation kinetics, KM is basically the concentration of substrate/ligand at which the rate of the reaction is half of the maximum rate (or the binding sites are half saturated).

The biophysical meaning of KM would depend on the underlying model. For example, in the equilibrium approximation of Michaelis-Menten model, KM is same as dissociation constant (of enzyme and substrate). In the Briggs-Haldane model (quasi steady state approximation), it is slightly complex: KM = (kr + kcat)/kf.

Overall, the thumb rule is that lower the KM faster will the reaction saturate.

  Is affinity always a function of the protein structure of enzyme? If
  someone study same enzyme in two different species and observe that
  the enzyme has different affinities in two species, then does it
  indicate that there might by slight difference in key amino-acid
  component at the binding sites of the enzyme between these two
  species?

Almost every property of the protein (not just affinity towards a ligand) is because of its chemical composition and structure. Although they are directly involved in binding, the amino acids at binding site are not the sole contributors to the affinity. The other amino acids that are critical for the overall structure of the protein are also important in preserving the function.


Can bioluminescence be used for cancer or tumor detection? What diagnostic applications, if any, are there in using bioluminescence to detect cancer or tumors (in vivo)?

Not in human but you can use this technique with genetically modified model organisms as described here.

The procedure is quite simple, you express the luciferase enzyme under the control of a specific promoter (specific for your cell type, like cancer) and provide luciferin via intravascular or intraperitoneal injection. The targeted cell type (for example cancer) will light up.

If you want to use that as a diagnostic tool in human you can't as the organism must express an enzyme catalyzing a bioluminescent reaction. Actually with the advance of genome engineering tools you might be able to do that even in humans (e.g. using CRISP/Cas9).

What is the advantage of bioluminescence over fluorescence? I might be wrong but I don't think there are any. I would rather express a fluorophore rather than an enzyme that requires a substrat.


meaning of binding capacity and binding affinity Actually, I am unfamiliar to biology, so when I read a thesis, the term "binding capacity" and "binding affinity" are really confusing.
Since my major is unrelated to biology, I don't know correct definition. Is there anyone who can explain differences between them clearly? Any references would be helpful, thanks!

Without any context... is hard to give a detailed answer.

I understand for bindind capacity the ability of a molecule to bind or attach to another molecule.
Binding affinity is the strength of the binding interaction between a single molecule and the other one.


Black/dark-red smooth West African worm, full of red blood This chap was strolling across my bathtub in Freetown, Sierra Leone, one day after very heavy rains and flash flooding. From its course, it appeared to have come up the bath plug from the drains.

It's about 2mm-3mm wide at the fattest points and 1mm wide at the thinnest points (which vary as it moves). It's maybe around 10cm in length. The picture's not the clearest but (to the naked eye) it looked almost completely featureless - smooth (no visible rings), and no obvious hooks or features at either end.

It was moving to the right from the point of view of the photo, and moved by narrowing and elongating unmarked segments about 2-4cm long each rather than the whole body. I say segments, since it seemed to be the same sections each time, but when it wasn't moving there was nothing to distinguish these segments. Its movements began by elongating the very front 2-3cm, then it'd feel around, come down, and other (unmarked) segments in the body would expand and contract to bring the rest of the body after it.

While I'm pretty sure it's not either of the two most notoriously nasty West African parasitic worms (Loa Loa or Guinea Worm), I didn't want to to take any chances, and we had nothing to isolate or store it in, so we carefully squashed this one after taking photos then cleaned the plug hole with boiling water and cleaner.

On squashing it, it burst in a very similar way to a recently-fed mosquito or bed bug with a splatter of what looked exactly like regular human/mammal blood. I've not seen this before from a worm. Each 5mm or so of worm body contained about as much blood as a well-fed mosquito.

I've done a little browsing of species of bloodworm but didn't find any obvious matches.

This might be unrelated, but the bathroom in which this worm surfaced has for several weeks had a small but constantly replenishing population of tiny flies like this, which I never questioned because they look almost exactly like regular drain flies. There's usually 1-3 of these flies on any given day, even after wiping out all of yesterday's flies, and I've not seen them anywhere else in the country. In this image it's about 3mm from wingtip to wingtip - much smaller than the worm.

There are not so many potential candidate worm groups with similar appearance, namely: (free-living) flatworms, Nemertea and annelids.

While there are several terrestrial and freshwater flatworms, some of which are quite long, they do not approach such an elongated vermiform body shape and their mode of locomotion is different. There are around two freshwater nemerteans in Africa, neither of which looks like your worm, and in any case most nemerteans move by gliding using their cilia.

So the remaining group is Annelida. There are three groups of annelids relevant in this context: polychaetes, oligochaetes and leeches. Polychaeta are predominantly marine and normally have more or less pronounced parapodia ("limbs"). Some of the do behave according to your description, but they are very characteristic in their appearance and you would not expect to find them in a bathtub.

What remains are oligochaetes and leeches. Leeches are more or less dorso-ventrally flattened and have very prominent suckers. Moreover a fed leech (from which you would expect large quantities of blood) would look swelled (the gut in leeches has diverticula).

So, the only worm group I can reasonably suggest is oligochetes. In fact your worm looks and behaves very much like a common earthworm. It is very typical of them to be highly mobile during and after rains and their blood pigment is hemoglobin (i.e. red). The only contradiction is that your worm had no clear true segmentation, but I believe, in some forms it is easy to overlook it.

The fly is indeed some species of Psychodidae.


Does the complimentary base pairing of rRNA with itself play a role in its transcription? I have read that the termination of the transcription of mRNA involves a termination sequence in the form of a stem loop. As the structure of ribosomal RNA involves extensive internal base pairing, I wonder whether part of the mature rRNA provides the termination loop for its transcription.

Summary

The process of the termination of transcription is still not well understood. It differs between eukaryotes and prokaryotes and between mRNA and rRNA. Although it involves stem-loop structures, such structures may be necessary, but are not sufficient for termination. The idea that the termination signal might be part of the mature functional transcript — especially for rRNA comes up against a number of problems, and turns out to be incorrect. Such problems include the extensive nature of the stem loops (which to use?) and the fact that the smaller stem loops emanating from the core conserved hydrogen-bonded skeleton, are not necessarily themselves conserved (reviewed by Brimacombe). In fact the large and small rRNAs are in a single transcription unit with other genes at the end of which are specific termination signals outside the region encoding the mature rRNA.

Prokaryotic rRNA transcription

This has been reviewed by Condon, Squires and Squires (1995). The structure of the well-studied rrnB operon of E.coli is shown below, with the promoters indicated as ‘P1’and P2’ and the terminator sequences as ‘T1’ and ‘T2’. (Adapted from Pfeiffer and Hartmann.)

This transcription unit includes the 5S rRNA as well as a tRNA.

Eukaryotic rRNA transcription

This has been reviewed by Goodfellow and Zoomerdijk(2012), from which the diagram below, of the mammalian rDNA repeat, is taken. The terminator elements are ‘T1–10’.

In eukaryotes the 5S rRNA is not in the same transcription unit as the large and small rRNAs (and the 5.8S rRNA). Indeed it is transcribed by DNA-dependent RNA polymerase III, rather than the DNA-dependent RNA polymerase I, which transcribes the rDNA repeat shown.


Examining milk for presence of harmful bacteria I am not experienced in diagnostic bacteriology and am interested in understanding more about it in the context of analyzing food purity.

For example, imagine I have a supply of raw milk which might be, for example, a 20 gallon tank. I would like to ensure that listeria, e. coli and salmonella are not present in the milk.

Is it sufficient to take a single drop of the milk and examine it under a microscope or do I have to do more extensive sampling, for example, sampling every inch vertically or something like that?

What is the procedure to make sure my milk is free of the bacteria, or is that impossible?

I am not interested in procedures to kill the bacteria. I know those. I want to understand the diagnostic processes to tell if bacteria is there.

A simple way to know if milk contains any bacterial contaminations is to take ~5 ml of the milk and add a couple of drops of methylene blue to it. If the milk is sterile, it will stay blue. If any bacteria are present they tend to take up the dye, leaving the sample colourless after ~1 hour. A more extensive way would be to plate 3-5 dilutions of the milk sample on LB or nutrient agar.
You don't have to do much extensive sampling. Just make sure that you take a couple of well-stirred samples.


Organisms that contain rare chemical elements By accident, I found a slide from a Polish chemical presentation, that talks about a small group of biological organisms which contain chemical elements not found in the human body, like:

B (boron),
F (fluorine),
Si (silicon),
V (vanadium),
Cr (chromium),
Se (selenium) and
Sn (tin).

Can someone provide a list of examples of organisms containing these chemical elements?

All the elements you mention (B, Fl, Si, V, Cr, Se and Ti) are listed as (probable) essential trace elements in humans by the World Health Organization. The WHO document "Trace elements in human nutrition and health" mentions a host of studies addressing the functions of these elements in species ranging from bacteria and plants to primates. The following list provides some of the functions these trace elements have in humans:

Boron - essential for cell membrane characteristics and transmembrane signaling (Nielsen, 1991);
Fluoride - necessary for the prevention of caries and it is associated with bone health (WHO);
Silicium - probably essential for healthy connective tissue and bone (WHO);
Vanadium - possible role as an enzyme cofactor and in hormone, glucose, lipid, bone and tooth metabolism (WHO).
Chromium - essential trace element that potentiates insulin action and thus
influences carbohydrate, lipid and protein metabolism (WHO);
Selenium - essential component of one of the antioxidant defense systems of the body (WHO);
Tin - expected to have a function in the tertiary structure of proteins (WHO).

References
Nielsen, FASEB 1991; 5: 2661-7
WHO, Trace elements in human nutrition and health 1991


Identify this large, beige or pine cone-colored squareish beetle and/or the pine cone it's on? I saw this large beige beetle on a large pine cone on the ground in February in Hsinchu county Taiwan.

It was about 4 cm long and 2 cm wide and the color was similar to the pine cone it was standing on. Though it was sunny it was cool (15 C) and the beetle didn't really respond when I picked up the cone.

I remember seeing a sign about (apparently) this species in November when hiking so I've attached it as well. I think the sign warns that this is a pest but I can't read it; I assume it is in Chinese.

Unfortunately I didn't remember the poster (from November) until later.

Any idea what it is and/or what the kind of cone that it's on, and what problems it can cause?

click images for full size

This is Tessaratoma papillosa, also known as the lychee giant stink bug. It is a pest for lychee trees, this is probably the reason for this warning sign. See the image for comparision:

See also this page for more information.


Spider identification This red spider has set up a web in my yard, in South Eastern, Texas, United States:

The spider itself is about an inch long (2.5 cm), and is predominantly red to brown in color, with red legs, and a very striking white line straight down the center of her back. The web is quite large—at least 4 feet (1.2 m) in diameter. It seems to be nocturnal, as I haven't seen it during the day, yet I've walked into the web (or nearly walked into its web) twice at night. Unfortunately, due to lighting conditions I wasn't able to capture the color particularly well.

I've searched but haven't found a species that looks like this yet.

After some more searching, I think stumbled across the answer. It appears to be an…

Eriophora ravilla:

Source BugGuide.net.

This species appears to have quite a diverse range of colors, and even thought I haven't found one that quite matches mine, the other similarities (the large abdomen, the stripe down the back, the four 'dimples', and the dark first leg segments) are enough to convince me. However, if anyone else can shed some light on this, I'd appreciate it.


Palm Tree Identification I need help identifying this particular palm tree. Unfortunately, I don’t have many details to give, and I’m by no means one to say I’m even an amateur at plant identification. We are unsure of its origin and can only confirm it’s age by how long we’ve resided here in Hockessin, Delaware. The plant is over the age of 14, and it stands a little over 12 feet high. The foliage is composed of single green shoots coming from the head of the plant which descend gracefully and reorganize into what one without knowledge would say is bark. We are looking to purchase another tree of this species or a close relative; there was a recent loss of an identical tree which sat opposed to this one.

Appears to me to be a Yucca tree, from the family Asparagaceae, whereas palms are typically a member of Arecaceae.


How is it decided that one drug is better than others by X times? I read in Tortora and Derrickson that :

  Enkephelins are 200 times powerful than morphine in their analgesic effects.

I wonder how exactly researchers arrive at a number (like 200 here). I also want to know what exactly is meant by "powerful".

In general, there is no universal way to quantify the effect of a drug; the quantification procedure depends crucially on what effect the drug is supposed to have. For example, if the drug is supposed to decrease blood thickness, then a measure of the drug's efficacy is a measurement of change in blood thickness upon application of a given concentration of drug. So I'll focus on the case of analgesics, since that's the context of your original question.

While I can't say for sure how this particular quantity was measured, it appears that the effect of analgesics like morphine or enkephalins is measured by direct measurements of pain under different administered concentrations of drug. This can be done in animal or human studies. In animal studies, varying concentrations of a drug are administered, and then the response of the animal to different pain stimuli is recorded. One common example of a pain measurement is a hot plate, where the animal's foot is placed on a hot plate and the time until it tries to remove its foot is measured.

These studies can also be done in humans. In this study (1), the effect of a particular drug was measured by different tests, including

electrical shocks of increasing intensity; maximum intensity of pain subject wanted to endure was measured.
pressure applied to the finger: maximum pressure subject wanted to endure was measured.
heat applied to the forearm (maximum tolerable temperature measured)
dominant hand immersed in ice water for up to 2 minutes. Subjects continually reported level of pain on a 0-10 scale, sum of all pain levels over course of experiment was used as measurement of total pain endured.
Tourniquet applied to cut off blood supply for up to 2 minutes, pain measured in same way as above.

If these pain measurements are recorded when the patient has different levels of the drug in their system, then comparing drug effects amounts to identifying the concentration of drug at which a particular pain response is achieved. In other words

  Drug A is X times more powerful than drug B if drug A causes the same effect on pain response (measured in some way like the ones measured before) as drug B at X times lower concentration.

As a side note, the initial thought I had was that this might be measured by quantifying the receptor-ligand affinity of the various drugs for the pain receptors (opioid receptors) in the nervous system. In that situation, saying that drug A was 200 times more powerful than drug B would amount to saying that A's affinity (or Kd) for a particular receptor was 200 times greater than B. Or something along those lines (see the Wikipedia article on receptor-ligand interactions). That would be a 'universal' way to measure drug efficacies, since a large number of drugs work by blocking certain receptors in the brain. But biology is too complicated to permit a straightforward relationship between binding affinity and perceived drug effect. At least, not yet!

References and Further Reading

(1): Luginbuhl M et al (2001). Comparison of Five Experimental Pain Tests to Measure Analgesic Effects of Alfentanil. Anesthesiology 95:22-29

(2): Jackson H. (1952) The effect of analgesic drugs on the sensation of thermal pain in man. Br. J. Pharmacol Chemother. 7(2): 204–214.

(3):Estrup Olesen A et al. (2012). Pharmacological Reviews 64(3):722-779 Extensive review of this subject.


Why does the slope of parent-offspring regression equals the heritability in the narrow sense? Background

---- Notations and assumptions ----

let $W_{ij}$ be the fitness associated to the genotype $AiAj$. $x$ is the frequency of the allele $A1$ in the population. The frequency of the allele $A2$ is $1-x$ because we'll consider only the case of a bi-allelic locus. Also, we consider that only one locus influence the random variable $W$ (the fitness). We will assume that the environment does not influence the fitness. We also assume random mating in order to use hardy-Weinberg equilibrium.

---- calculations ----

The mean fitness is:

$$\bar W = x^2W_{11} + 2x(1-x)W_{12} + (1-x)^2W_{22}$$

The variance of fitness is:

$$\sigma^2 = x^2(W_{11}-\bar W)^2 + 2x(1-x)(W_{12}-\bar W)^2 + (1-x)^2(W_{22}-\bar W)^2$$

We then want to calculate the covariance between father and son with respect to fitness.

Suppose first that the father is $A_1A_1$ Then the son will be $A_1A_1$ if the mother transmits an $A_1$ gene to him, an event with probability x. Similarly the son will be $A_1A_2$ with probability $1-x$. The father himself will be $A_1A_1$ with probability $x^2$. Continuing this wa it is possible to draw up a table of the probabilities of the various father-son combinations in genotype and hence fitness.

Therefore, assuming no change in frequency of $A1$ between the two generations, the covariance father-son is:

$$cov = x^3W_{11}^2 + 2x^2(1-x)W_{11}W_{12} + x(1-x)W_{12}^2 + 2x(1-x)^2W_{12}W_{22} + (1-x)^3W_{22}^2-\bar W^2$$

which also equals

$$cov = x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2$$

The correlation between the two fitnesses is found by dividing the co-variance by the variance (since the variance of sons is the same as that for fathers):

$$cor = \frac{x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2}{\sigma ^2}$$

We then define dominance and additive variance:

$$\sigma_D^2 = x^2(1-x)^2(2*W_{12} - W_{11} - W_{22})^2$$

$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$

such as

$$\sigma_D^2 + \sigma_A^2  = \sigma$$

My question

The slope of a parent-offspring regression equals the heritability in the narrow sense $h^2_N$.

Heritability in the narrow sense is defined as $h_N^2 = \frac{\sigma_A^2}{\sigma}$ (see Why is a heritability coefficient not an index of how “genetic” something is?).

We defined above that the correlation between parents and offspring is $cor = \frac{cov}{\sigma}$. So I'd expect the slope of the parent-offsprings regression to equal $cor = \frac{cov}{\sigma}$ and not $h_N^2 = \frac{\sigma_A^2}{\sigma}$

What am I missing? Is there a mistake in my background calculations? Is there a mistake in the way I defined some concepts? The answer might be much simpler than it looks like!

Well, I think I found the very simple mistake I made…

Looking again in my equations, I realize that (for some reason) $cor = 2 \cdot \frac{\sigma_A^2}{\sigma}$

And looking at this website, I see that the slope of the parent-offspring regression is $\frac{h_N^2}{2} = slope$

Here was my mistake!


Are humans the only mammals that are known to display homosexuality? REQUEST: In this post I do not refer to, nor do I encourage reference to, any ethical/moral/emotional aspects of homosexuality. So please don't start an pro/anti- LGBT campaign in the comments section.

Are mammals (other than humans) known to engage in homosexual activity of any sort?

From the way I see it, homosexual activities carry no evolutionary or reproductive benefit: No offspring produced, no continuation of species...hence pointless.

Yes, I get that the "need to mate and to produce and protect offspring" is hard-wired into every (normal) mammalian brain. If I've interpreted this correctly; intercourse is a fairly energy-expensive act so if there were no immediately clear "incentive" for mammals to mate they wouldn't mate at all, hence heralding the decline and eventual extinction of a species. Nature solved this conundrum by ensuring that the brain would perceive intercourse as highly pleasurable, thereby securing the necessary "incentive" for mammals to mate.

The only "flaw" here, is that simply stimulating the genitals is sufficient enough to elicit a sensation of pleasure. So there's no real need to go through all the trouble of finding a suitable animal of the opposite sex and "do it" to feel good. A sufficiently intelligent mammal would soon figure that out; so this opens up two more possibilities: 1) Masturbation and 2) Homosexuality. (Since this post's on Homosexuality, I'm only going to deal with the latter)

So, a mammal intelligent enough to figure this out would have three options before it : 1) Heterosexual activity, 2) Masturbation, 3) Homosexual activity; the last two options being a way to bypass Nature's original intent.

So before I continue, I want to make what I mean by "homosexuality" very clear:

a) A being that displays option 1) or both 1) and 2) is heterosexual.

b) A being that displays options 1) and 3) [and maybe 2) too] is bisexual.

c) A being that displays option 3) or both 3) and 2) is homosexual.

[Just to make it explicitly clear, a homosexual will always steer clear of option 1)]

So let me just put all of that together and re-phrase my question:

Q- Are there any known instances where a (non-human) mammal consciously avoids heterosexual acts and instead prefers to engage in homosexual activity

Personally, I find this doubtful, since the existence of homosexuality (among humans) is the unintended result of Human self-consciousness/intelligence, something that other mammals apparently lack.

HOWEVER: (Considering another possible reason for homosexuality)

If occurrence of homosexual tendencies is (also) due to, say, the stochastic, faulty "hard-wiring" of the human brain due to mutation or damage to neural tissue (I'm not sure if this really is one of the reasons for homosexuality), then it would seem plausible that other mammals could also be affected by this stochastic "fault" and thereby display homosexual tendencies.

Although intuitively it would seem unlikely that there could be an evolutionary advantage to homosexuality (other than some theories regarding population control), homosexual behavior has been clearly observed in a variety of birds, monkeys and apes, lions, dolphins, lizards, insects, and plenty more.

The case of the bonobo is particularly striking in that homosexuality and bisexuality are more common than heterosexuality.  According to this Wikipedia article:

  Bonobos, which have a matriarchal society, unusual among apes, are a fully bisexual species—both males and females engage in heterosexual and homosexual behavior, being noted for female–female homosexuality in particular. Roughly 60% of all bonobo sexual activity occurs between two or more females. While the homosexual bonding system in bonobos represents the highest frequency of homosexuality known in any species, homosexuality has been reported for all great apes (a group which includes humans), as well as a number of other primate species.

Although the complexity of sexuality likely points to the existence of multiple genes playing a role in sexual behavior and preference, at least one study$^1$ points to a single gene playing an important role in the sexual behavior, of female mice:

  In this study, we generated mutant mice specifically lacking the FucM gene that encodes fucose mutarotase. The homo- and heterozygous mutant females exhibited deficits in sexual receptivity as demonstrated by a drop in lordosis score. Moreover, the mutants displayed masculine behaviors and preferences to female urine over male urine.

1) Male-like sexual behavior of female mouse lacking fucose mutarotase, Dongkyu Park, Dongwook Choi, Junghoon Lee, Dae-sik Lim and Chankyu Park, BMC Genetics201011:62, DOI: 10.1186/1471-2156-11-62


Can I use multiple bicistronic RBS sequences in a synthetic biological circuit? The bicistroninc RBS sequences (BCDs) developed by Mutalik et al. [1] aim to remove context sensitivity from translation and therefore ensure more predictable gene expression. However, I have been told that having multiple transcriptional units, each using BCDs, can make cells sick. The explanation that I was given was that the toxicity is from small peptides that are produced from transcription from the first RBS sequence.
Has anyone demonstrated toxicity from multiple BCDs or is it apocryphal? If it has been demonstrated, is the mechanism of toxicity known and is there a way to use multiple BCDs while maintaining healthy cells?
[1] V. K. Mutalik et al., “Precise and reliable gene expression via standard transcription and translation initiation elements,” Nat. Methods, vol. 10, no. 4, pp. 354–360, Apr. 2013.

That’s a great question and has lot of opportunities to explore. I am not sure anyone has followed up on this original BCD work systematically. We did try cloning these elements on a medium copy plasmids, in an operon design, driving multiple genes, and now I think about it, that was not a smart thing to do. Cloning was very challenging, probably due to toxicity you mention. Didn’t have time to investigate this in depth (that it self is a cool project), but I think the toxicity is due to too much resources (ribosomes?) titrated out on these units. But that’s a hand-wavy explanation. Need mechanistic study to investigate. I think Tom Ellis’s group and others have done some beautiful work on toxicity associated with protein expression. Personally I think the toxicity is not related to the inert peptide (1st gene in a BCD operon) that’s produced. Another story we tried was to replace this first gene with something functional but not published.
Coming back to using BCDs for driving multiple genes, I would say if you clone these directly on genomes they should work like charm. We did try this and works good. Not published much (oh god, that’s so much work unpublished!) Bacterial operons have these junctions and elements of different strengths. Happy to discuss more if you have a follow up question!!
Thanks for your interest in this work. Really proud of our work on this system. Of course happy that we did this work as there were so many early effort on these BCD type elements. And love this open discussion SE platform! Don’t know how synbio survived without this system of sharing knowledge and experiences. Best wishes
Vivek Mutalik