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Refutation of Darwin's Random Evolution Theory
I saw this refutation online of Darwin's Random Evolution Theory and cannot see any holes with the logic. Can anyone crack this simple refutation?

Refutation of the Theory of Random Evolution
As for the theory of evolution, which says that living things evolved progressively from
  mud - first organism - bacteria - fish - animals - humans through tiny
  random mutations which were advantageous and naturally selected;
  there's a lot to say on this. All currently living life forms appears
  to be highly related, sharing the same DNA system and cell structure.
  This would suggest a common first ancestor as the theory suggests (or
  better yet - one Designer), however, the most obvious flaw with the
  theory is that the first organism must have had highly sophisticated
  intelligent design. There is a minimum requirement for even the most
  primitive possible life form, without which it could not possibly
  survive.
Minimum Requirements for First Organism

The first organism must have a system of producing and/or sourcing energy along with subsystems of distribution and management
  of that energy which interact and work together, otherwise it cannot
  power critical tasks such as reproduction.
It must have a system of reproduction which necessitates pre-existing subsystems of information storage (DNA), information
  copying, and information reading/processing which interact with each
  other and work together. This reproductive system is dependent on a
  power source, so it must be coordinated with the power system. The
  reproductive system must also copy/rebuild all critical infrastructure
  such as the power system and the reproduction system along with the
  "circuitry" and feedback mechanisms between them, otherwise the child
  organism will be dead..
It must have a growth system, otherwise the organism will reduce itself every time it reproduces and vanish after a few generations.
  This growth system necessitates subsystems of ingestion of materials
  from the outside world, processing of those materials, distribution,
  and absorption of those materials to the proper place, building the
  right thing at the right place and in the right amount. It must also
  have an expulsion system for waste materials.
The growth system must also be coordinated with the reproduction system. Otherwise, if the reproduction trigger happens faster than the
  growth, it will reduce size faster than it grows in size and vanish
  after a few generations. The growth system also requires connection to
  the power infrastructure to perform its tasks.
All the "circuitry", signaling, and feedback infrastructure which allows the different systems and subsystems to coordinate
  together and work together must be in place before the organism can
  "come alive". The reproduction system won't work without coordination
  with the growth and power systems. Likewise, the power system by
  itself is useless without the growth and reproduction systems and
  cannot survive. Only when all the "circuitry", etc. is in place and
  the power is turned on is there hope for the hundreds of
  interdependent tasks to start working together. Otherwise, it is like
  turning on a computer which has no interconnections between the power
  supply, CPU, memory, hard drive, video, operating system, etc -
  nothing to write home about.
We assume it originated in water since gas is too unstable and solid is too static. If so, the organism must be contained by some
  kind of membrane otherwise its precious contents will drift away in
  the water due to natural diffusion or drifting of water due to
  temperature variations in the water from sunlight, etc. or from heat
  generated through its own power, or wind, moon, etc. If so, this makes
  the assembly of such an organism more problematic, since it would need
  to be closed shut before it can build itself in a stable way. Yet, to
  build itself it would need to be open for a long time until all
  systems are built and interconnected.

From the above minimum requirements it is clear that the simplest
  possible surviving organism is by no means simple. You would need
  thousands of different proteins/lipids etc., in the right proportions,
  all intricately folded and actively interacting with each other and
  with sophisticated organelles. Contemplate this and you will see the
  necessary complexity of this primitive organism is far more
  sophisticated than anything modern technology has ever produced. Even
  the most sophisticated Intel CPU is mere child's play compared with
  the design of such an organism.

See this question

As explained by @5th below, this is really about the origin of self-replicating systems. See here for an outline discussion of this difficult problem. (added later - I have just seen your other question, so now realise that you know all of this anyway!)

thank you to all who answered/commented. I see its not so simple as I thought. still seems to me a far jump to go from things like self replicating RNA to fulll fledged single cell organisms. intuitively, i just dont see how it can evolve one tiny step at a time due too many interdependent things. will need to think it over

@user1909257 I think your stumbling block is that you don’t account for the vast time span involved. I’s very hard to grasp how much time evolution had. We can estimate the rate of evolution from experiments and observation, and let me tell you, even though evolution is happening really slowly, there was plenty of time since the beginning of the world. It’s simply unimaginable how old Earth is. The book Climbing Mount Improbable illustrates how tiny changes can accumulate over time.

Theory of evolution has not to be called theory of random evolution! Mutation is a random process (more or less) while natural selection is not random but is a deterministic consequence of the effect of alleles on their own replication abilities. Then, origin of life is not part of the theory of evolution. Theory of evolution has a domain of definition (just like any theory). It explains how living things evolve and it does not say anything about the big bang or the origin of life. But still, talking about the origin of life is worth and for this point your question is interesting.

Apparently it's still active. I think it should have been closed initially but better late than never.

I like @5th 's answer but I thought it might be worthwhile to clarify on some points and pull the logic out a bit more.
First there is some contesting the overall logic that it assumes all these qualities of life are showing up at once.  If they had to, it probably is true that life could not evolve, but the general assumption is that there is a path to do so.  Let me try to be convincing of this.
Dawkin's theory of the replicator is axiomatic and not entirely helpful at this point, but it does have a lot to say.  Once you have self replicating systems, the rest of biology and evolution and selection does seem reasonable, even with the emergence of complicated structures like the eye, the flageller motor and other seemingly unplausibly multi component systems seem to magically come together and do something new in the course of evolution.  Dawkins wrote a book on this topic "Climbing Mount Improbable" on this topic which tries to answer this question for several cases.
To outline why biological systems can and do seem to leap to new abilities, organs and unprecedented assemblies. In fact the do not, but there are so many possible trials (quintillions? ) over the trillions of years, that eventually some adaptive path to these features, which has usually been found when we go looking for it.  As such there is no clear reason why new cases of this argument need to carry extra weight.   The argument of statistically improbable combinations has been tried and remains unconvincing with respect to evolution several times.
After this, I think it would be fair to say that the origins of life, although coming clear still has many details to be resolved, but progress is being made. Precambrian evidence of primitive life was very different as seen in fossil records.  We can see that at one time there were only bacteria and single celled organisms.  There is evidence that at one time there appears to be only simple very large single celled organisms that lay in shallow water and soaked up the sunlight, growing and growing.
We can see that going back about 1.2-2 billion years, life shows a pretty clear progression where selection and adaptation creates complexity in living things and transitions life from exclusively chemotrophs (metabolizing Sulfur from geological processes) to anoxic (no oxygen environment) photosynthesis, and then oxygen breathing organisms.
In the precellular world, the RNA World hypothesis describes how all that life needed was one sort of molecule - RNA.  That is chemically a very simple replicator.  Evidence is pretty strong that RNA world was possible.  Many chemists are interested in proving that RNA can be created more or less spontaneously from early earth chemical environments and recent experiments show that spontaneous soups containing RNA are a reasonable picture of earth at one point.
All this being said its probably true that exactly what happened and how it happened will never be 100% known and the argument can be made that something unnatural happened at some point. But I hope you can also see that while the argument may still hold some water, the need for any magical interventions in the action of life is retreating to a point of origin - the beginning of time.  Scientific inquiry is very much focused on filling the picture of the origins of life on earth though and given the success of finding probable paths through to the origins of life, the odds actually are in favor for making a statement of the physical mechanisms of life's origins.
Just a couple of side notes.. (1) biologists are not stuck on everything being random.  There is lots of work on mechanisms evolved to adapt in non-random ways.
(2) Darwin is not a sacred cow - just about any working biologist would love to show Darwin was wrong even in a little way.  The same is true for Einstein, Newton and the rest.  After a few years of trying though what one usually finds that its kinda difficult.  Its not a matter of who makes the argument or what it means, but it has to be convincing and that turns out to be difficult.

i agree that the answer is not so clear cut, and ultimately may remain a mystery

science is more guessing than proof in many cases, theories are built on lots of different evidence that somehow turns into a story.

(A few words about your source: it's little use to come a serious site about science and quote sources whose objective is to prove the existence of god. If you want to learn more about the beauty of life and the theory of evolution, I suggest you read the book "The Blind Watchmaker" by Richard Dawkins, it's an excellent introduction to the topic.)
There is no such thing as "Darwin's Random Evolution Theory". Further, Darwin put forward a theory of the origin of species (which is the opposite of random!), not of the origin of life (I do believe he did not write anything at all about how life develops from "mud".)
Thus, there is nothing to "crack" in that "logic", because the question is not valid in the first place.
Disregarding that the question is not valid in the first place, I think you're trying to refute the idea that self-replicating life-like things could emerge spontaneously. I'm not sure there is anything particularly random about how the world behaves, it's rather a label for what human imagination and ingenuity cannot predict. However, in the sense of random you are using, self-replicating patterns (I won't be the one to determine whether it passes as life) have been shown to be possible in a much simpler world than ours: Conway's Game of Life. A pattern that uses a kind of instruction tape, replicates and destroys its parent (repeating this every 34 million generations) was found in 2010 by Andrew J. Wade.
http://en.wikipedia.org/wiki/Conway%27s_Game_of_Life#Self-replication
If this can occur, although to a large part it was probably designed in this case, you cannot say it is impossible in a world on a much larger scale and over eons of time (these kinds of time periods cannot easily be imagined - a good reason why we tend to believe it is very unlikely that something very improbable will happen during the period).

what is the difference between origin of species and origin of life?

The first talks on how and why life changes over time. The second talks about how to make life. It is the difference between how prosperous nations are run and how to win a nation its independence.

I saw this refutation online of Darwin's Random Evolution Theory and cannot see any holes with the logic. Can anyone crack this simple refutation?

Certainly. First and foremost: The refutation is not simple. It is a complex argument that draws consistently on baseless assumptions and relies on the lack of education of the reader to get its point across. I do not mean that the reader is dumb, merely that the author's target audience is probably ill-informed about the details of Biology, Chemistry, Physics, and similar fields. The author relies on being long and convoluted, appealing to faulty logic, and a whole slew of fallacies that might be missed if the reader hadn't already encountered them in the context of Evolution.

As for the theory of evolution, which says that living things evolved progressively from mud...

Well, as 5th has already said, this is a bad start. The Theory of Evolution (via Natural Selection if we want to get the full name out there) says nothing about the beginnings of life. That would be Abiogenesis.
The Theory of Evolution merely dictates that subsequent generations adapt to their environment, and that those who have adapted best will pass their inheritable traits to the next generation.

1. The first organism must have a system of producing and/or sourcing
  energy along with subsystems of distribution and management of that
  energy which interact and work together, otherwise it cannot power
  critical tasks such as reproduction.

This isn't a difficult task. Currently the most abundant source of energy on the planet is the Sun. It has been shining for billions of years before the Earth was formed, and will be shining for billions of years after you've read this paragraph.
If we exclude sunlight for the LCA (Last Common Ancestor) of all life, then we're mostly talking about geothermal energy or chemical reactions. Ultimately, though, extant organisms store energy in chemical bonds. The primary "Energy Carrier" of the cell is ATP - Adenosine Tri-Phosphate, and it's the third of the three Phosphates that is often "harvested" for its energy - leaving ADP as a product of metabolic reactions.
That a system of sourcing and managing energy distributions could arise from even simple situations is not so far fetched. Consider the Earth's atmosphere and weather patterns; initially they appear extremely complex and result in myriads of environments that even modern science cannot accurately predict more than a few days ahead.
However, the entire system is driven by the interaction of the planet's geography, the gases composing the atmosphere, and the Sun as it heats the system. Regulation is taken care of by Physics - hot air rises, cold air sinks, geographical location determines exposure to the energy source, etc.
Power is not an issue. Basic regulation is not an issue. Once the basics are down, more complex forms can Evolve.

2. It must have a system of reproduction which necessitates pre-existing subsystems of information storage (DNA), information copying, and information reading/processing which interact with each other and work together. This reproductive system is dependent on a power source, so it must be coordinated with the power system. The reproductive system must also copy/rebuild all critical infrastructure such as the power system and the reproduction system along with the "circuitry" and feedback mechanisms between them, otherwise the child organism will be dead..

If you're willing to accept that chemical reactions between amino acids and similar molecules can occur on primitive Earth, then the jump to this question isn't that hard.
First, you should know that DNA almost certainly wasn't the initial genetic storage form. A commonly accepted and incredibly intriguing theory is the RNA World Hypothesis. RNA can also store genetic information - albeit at a less accurate rate for a shorter amount of time. More importantly, RNA has also been observed folding into itself to create proteins and catalysts. It's sort of a jack-of-all-trades, and since it's basic constituents have been discovered amongst the vacuum of spaces, all the pieces were here on Earth 4 B.Y.A. to make some of the first steps towards organic life. All that had to happen is that the right molecules had to come together, then physics takes over and you have some astonishing reactions. Given the right conditions and a few hundred million years, who's to say it isn't possible?

3. It must have a growth system, otherwise the organism will reduce itself every time it reproduces and vanish after a few generations. This growth system necessitates subsystems of ingestion of materials from the outside world, processing of those materials, distribution, and absorption of those materials to the proper place, building the right thing at the right place and in the right amount. It must also have an expulsion system for waste materials.

Let me introduce you to the Micelle: A naturally occurring structure that looks an awful lot like today's cell membranes. It doesn't require exotic materials, it doesn't require fancy catalysts; it requires amphipathic molecules and that's about it.
While complex organisms do require subsystems and various ways to ingest food to harness nutrition, for the most basic forms of life "Digestion" is little more than taking in outside material into the cell and then putting what's left back outside.
To that end, Micelles merge on their own when distance allows. The mechanism is powered by the entropy of the water molecules surrounding the micelle's structure and doesn't require any sort of metabolism or organic control to occur. In addition, hydrophobic molecules can slip through unhindered fairly easily (depending on size), and many of amino acids used to make proteins and micronutrients our current bodies require are hydrophobic.
So it's entirely possible to have a basic membrane that can "eat" other things without being strictly alive. Everything after that is just added complexity that was retained due to improved functionality. It's important to remind yourself that we're talking of a span of hundreds of millions of years. Almost nothing currently living on the planet has gone more than a few hundred thousand or few million years without drastically changing how it looks. A hundred million years ago humans were little more than rats or furry lizards. Imagine what could happen with 5x that span!

4. All the "circuitry", signaling, and feedback infrastructure which allows the different systems and subsystems to coordinate together and work together must be in place before the organism can "come alive"...

This very, very much depends on your definition of alive - which is still difficult to define for Biologists to this day.
Are viruses alive? They certainly do not retain any reproductive ability of their own and must hijack the operations of a living cell to create the next generation - but they still have inheritable genetic material, they still create structures and adapt to their environment, and still - in an odd way - consume resources to reproduce.
What's the difference between the spread of iron oxide (rust) -- which, you could argue, requires an interaction of existing elements to perpetuate and has built-in feedback (it is inhibited when there is a lack of a substance - a completely viable and well-known trope of feedback mechanisms) -- and the spread of a fungus, which you could describe just as simply?
Defining "Life" by what exists today is a mistake often made by those who dispute the Theory of Evolution. Only the most basic assumptions and connections can be made between life as-it-exists and life-as-it-started. The planet is different, the air is different, the Moon is significantly further away, and countless other things have occurred.
That said, we have definitely observed complex interactions of molecules and systems in situ within conditions similar to those of early Earth. One of the most famous is the Miller-Urey experiment. If you're asking why they didn't succeed in creating life, remember that it took about 500 million years for the LCA to spring into existence... And the LCA is not necessarily the first form of life, just the one that gave rise to all current forms. Miller and Urey experimented for two weeks, not 500 million years, but still made significant discoveries in that short a time-span.

5. We assume it originated in water since gas is too unstable and solid is too static. If so, the organism must be contained by some kind of membrane otherwise its precious contents will drift away in the water due to natural diffusion or drifting of water due to temperature variations in the water from sunlight, etc. or from heat generated through its own power, or wind, moon, etc.

We have already discussed the Micelle above.

This refutation contains a fundamental error.
The first living organism need not be anything complex, it just has to bea molecule that creates copies of itself which inherit its characteristics.
From there its population grows exponentially and evolution starts.
Therefore there is no need for any of those items he is listing as requirements for the first life.

your system works for simple molecules. but to go from there to interdependent intelligent design is a long way. consider upgrading your software through random mutations of the hard drive. it's just impossible for anything to improve unless its coordinated with other changes in an intelligent way

for example, you cannot improve the code for windows xp by randomly changing one line of code. the reason being that this change would affect other lines of code and you'd need to modify those in a coordinated way. make sense?

I am pointing out that this so-called refutation is flawed as it assumes that first life must be someting complex. As for the continued evolution of life you can start a different thread.

simple molecules is not first life.

No but molecules that create copies of themselves which inherit their characteristics are. And that is all that is necessary for first life.

thanks but dont you think, you need some kind of "intelligent design" at some point. meaning, something which is highly interdependent and sophisticated. don't see how that could work thru random mutations. you'd need some kind of coordinated design.

At some point is a different matter. The question is about the origin of life. If you want to have a discussion about the process after life has originated then that should be in a different thread.

Continuing to say "you need some kind of intelligence" doesn't mean you have demonstrated it to be so.  Yes, it's a long stretch from self-replicating chemicals in a micell to full-blown organisms with brains capable of intelligence, but you also have a VAST amount of time, and a VAST amount of attempts with which to make incremental changes.

@user1909257.. yes you can... make a random change in XP code. Do so for 1000 copies. Send it to users. The copies that work, have their code copied 1000 times more with additional random changes. The copies of XP that do not work are thrown away. Do this every day for least 10 million of years.we actually have self evolving code... that have done things like build a TV antenna, fly a fighter plane, and even play chess. What you are missing is selection after that random mutation. Only the best live and breed, everyone else dies.


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Can we disambiguate competing molecular mechanisms of learning and plasticity by measuring electrical activity of neurons?
I have been reading with fascination about the several molecular- and cellular-scale mechanisms and structural changes that underlie what we refer to as long-term plasticity. For instance, [1], [2], [3].
In particular, there seem to be at least: synaptic scaling, synaptic pruning, synaptogenesis, spinogenesis, neurogenesis.
My questions:

How do each of the above mechanisms/ events affect the classical extracellular single/ multi-unit spikes, postsynaptic potentials (LFPs), and local electric fields? Does a mechanistic forward model exist, which specifies the biophysical transformation from synapse-level changes to spikes and LFPs? Are there spike simulators out there that model these properties?
Using such a forward model, can we solve a statistical inverse problem to infer anything at all about these LTP/LTD-induced small-scale structural and functional changes?
For instance, one metric of analysis could be: post-spike-time filters (self-terms and cross-terms) inferred using statistical point-process models. Another could be the shape of the action potential itself, which is typically used only for spike sorting, and then discarded.
Has something along these lines been done? Or is it infeasible? If so, why?
Finally, If anyone could give a brief overview of the gamut of synapse-scale physiological/ imaging techniques used to characterize these mechanisms, I would be very grateful!

this is a pretty broad question. I can answer parts of it, but it would be insufficient overall. If you can break the question down to smaller chunks, you may get better responses.

Thanks Memming. I need to do some more reading and thinking to break down the question. Will do. Feel free to share some thoughts in the mean time.

Just adding a little bit here. Estimating changes in connectivity based on STDP is hard
http://klab.smpp.northwestern.edu/wiki/images/2/2b/Stevenson_Inferring_Plasticity_2011.pdf
but yes - these questions are enough to keep a big field busy for a long time.

Thanks!
I was thinking along the following lines.
(1) Write down the cable equations for neurons within a network, given: anatomical layout of the network, spatial distribution of dendrites, spines, synapses, and synaptic strengths (forward model).
(2) Acquire joint microscopy + electrophysiology dataset.
(3) Invert the forward model with synaptic strengths as free parameters.
(4) Track these inferred parameters over time or compare them between conditions.

Yes, that could be a strategy. I like your idea. But, you'll need to record from pairs of connected cells intracellularly which is not impossible, but limits long stable recordings. I guess imaging techniques may be able to get over this limit.

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Do the mother's genes determine the sons' (heredity) intelligence more than the father's?
It is a general belief that a person's intelligence is determined by both nature and nurture.
I can find a study by Turner 1996 ( in fact, this is the motivation of this question), which makes the claim that since several genes which determine intelligence appear to be located on the X chromosome, the one men inherit from their mothers, and since a man only has one X chromosome inherited from his mother, so that's why mom's intelligence is very important to her sons, even more so than the father's!
Thus, my question is, do the mother's genes determine the sons' inherited intelligence more than the father's, as claimed by the above paper? In other words, a man inherits less intelligence from his father than from his mother? Note that I don't discount the possibility that the father could have helped to raise his son's intelligence by actively nurturing him in the correct way, just that as far as the "intellect genes" ( if there are such things) are concerned, the father plays less role than the mom.
A similar question is asked at Skeptic.SE, but it is geared more towards the contribution of mom's genes against all factors that account for son's intelligence, nurture and nature. My question is focused exclusively on the contribution of mom's genes vs. dad's.
Any new research on this front?

You might want to take a look on the wikipedia site for x-linked recessive inheritance. The article by Turner mentions that out of 325 known recessively inherited genes associated with mental retardation, 17 are positioned on the x-chromosome. In case you are a male and have one of these seventeen recessive genes on your x-chromosome causing you in some way to be less intelligent, you must have inherited that gene from your mother. In those cases it is more like you inherit "stupidity" genes from your mother, who might be an unaffected carrier of the stupidity gene due to the fact that she has two X-chromosomes and the gene causing mental retardation is only present in one of those x-chromosomes.
There might of course also be recessive genes on the X-chromosome causing males, who has only one X-chromosome, to be smarter but genes that are not causing disease might not be so interesting to investigate from a medical point of view.
According to wikipedia there are 499 x-linked genes and the total number of "vaguely defined traits" are 983.
I would say that yes, as a man you inherit more genes from your mother than from you father affecting your intelligence due to the fact that some genes on your x-chromosome affect your intelligence. Whatever the 499 x-linked genes do, you could say that traits affected by those genes to a greater extent are determined by your mothers genes than by your fathers, if you are a male.
Technically you would of course also have to take the genes on the y-chromosome, which are much fewer, into account.

If we approximate that the human male genome has a total of 20000 protein coding genes, the x-chromosome has 800 protein coding genes and the y-chromosome has 60 protein coding genes a male gets on average (19940/(19940+19200))*100 = approximately 50.945 percent of his protein coding genes from his mother. Now for a highly polygenic trait depending on genes homogenously distributed on all chromosomes one would naively expect that 50.945 percent of the genes contributing to that trait is inherited from his mother.

Intelligence is a highly polygenic trait and genetic variants affecting intelligence appear to be (very roughly) uniformly distributed over all chromosomes. If intelligence is inherited more from the mother than the father, the actual effect of this difference appears to be negligible. (This is also evident from simple studies that test mother-child and father-child correlations, and they find no difference)

Do genes/genetic variants on the y-chromosome contribute as must to the total variation of intelligence in males as the genes/genetic variants on the x-chromosome even though the y-chromosome is much shorter? You inherit genes you do not inherit "intelligence".

No, since the y-chromosome is much smaller, it is expected to contribute less to the variance. But what I'm saying is that the of the total genome, the X-chromosome is only a small fraction of it. Hence, if mothers contribute more to the inheritance of intelligence, then this bigger contribution is at most negligibly larger. We have simple studies that check the correlation of intelligence (or height, or other highly polygenic traits) of father-child and mother-child, and no difference tends to be found. Hence, there can be at most a small difference in contribution.

In Lee et al, 2018 they look at genome association of educational attainment (which is highly correlated genetically with intelligence). In the Manhattan plot you can see a rough "genetic architecture" of the trait in question, and one can see that it is widely distributed over the entire genome. They also analyze the contribution of the X-chromosome.

@Eff, you would like to expand on your comment and make it into an answer?

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Are there eukaryotes without introns?
This question on the function of introns in eukaryotic genes made me think: I know that more basal organisms have smaller introns and fewer alternatively spliced exons compared to mammals. But are there eukaryotes whose genomes have no introns at all?

Well yeast has very very few if that counts. See here. I recently checked the number if annotated isoforms for 5592 yeast genes and NONE of them had more than one!

I don't believe so.  I have never come across a eukaryote that does not have introns although there are some genes that do not contain introns.  Some eukaryotes like ciliates actually contain other non-intronic intergenetic regions that seem to be nonfunctional.  These are called Internally Existed Sequences and are removed from the germ-line active micronucleus before going to form the transcriptionally active micronucleus.  Interestingly, introns are also present in these organisms and are present in both the micro and macronucleus.  These introns are spliced out in textbook fashion.  I believe one of the organisms where introns was discovered was in Tetrahymena thermophila with the intron in the rDNA sequence.

Could you expand with some examples?

@nico: examples of what, eukaryotes with introns or eukaryotic ciliates with non-intronic intergenetic regions?

thanks for the edit, I was speaking about the ciliates, as I did not know about that.

@nico, Tetrahymena thermophila's macronucleus contains about 15,000 copies of the gene that encodes for the ribosome.  I believe it was in this gene sequence that introns were first discovered.  The Nobel Price for the intron discovery was shared with another person as they both discovered it in different organisms about the same time.


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Can life subsist on anything else but water?
Inspired by an answer to a previous question.
It's hypothesized that extraterrestrial life could be based on silicon rather than carbon as its main structural element.
Are there similar theories about an alternative "life solvent" rather than water?

Ha, I was just about to ask the very same thing having read the same question!

Some scientists are indeed working toward inorganic life see here, bottom part. Not that they succeeded yet, but it's an active research field.

This is not a definitive answer.
The solvent closest to water in its properties such as dielectric constant, melting/boiling points, etc are formamide and sulphuric acid.
                        F       S       W
Melting point (⁰C)      2       10      0
Boiling point (⁰C)      210     337     100
Dielectric Const        109     84–100  80
Specific gravity        1.133   1.94    1

But water is the simplest i.e made up of only two types of atoms (Which are decently abundant).
Regarding silicon: even though silicon can undergo some level of catenation (silanes) it is not comparable to carbon. Silicon can form polymers like silicone (poly-siloxanes). But I think carbon seems to be more versatile. It is also more abundant (check this out. A nice representation of abundance of different elements in the universe)
Also check this out: it is about exoplanet habitability.
Since certain elements are more abundant than others, the likelihood of them giving rise to life is higher. Therefore water seemingly emerges as the life solvent.
[still most times we see everything in an earth point of view]


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Do birds have navels?
This picture shows the development inside a bird egg:

This shows the connection of the embryo to the yolk sac.  Does this mean birds have navels?  And if so, what happens to the umbilical cord once the bird hatches?

All animals develop in this way, whether they are oviparous (developing in an egg) or viviparous (developing inside their mother, or live-birth).
From Wild Birds Unlimited:

All mammals have navels or belly buttons where the umbilical cord distributes nutrients between a mother and her fetus. After birth, the umbilical cord is cut and a scar develops on the abdomen where the hole closes.
Of course avians or birds hatch from eggs which are virtually self-contained life-support systems that only require warmth and oxygen to develop properly. Instead of an umbilical cord scar, birds have yolk sac scars at hatching. This is where the chick embryo is attached to the yolk sac. But don’t look for any bird belly button rings. The scars usually heal and become virtually invisible.

As for their umbilical cord, it looks like it falls off when the chick hatches if it is not fully absorbed along with the yolk sac, along with everything else contained in the egg (although there is not a lot of material left within the egg by the time the chick is ready to hatch).

Inside a bird's egg there is a tiny cord that connects the developing embryo to the yolk sac. When the egg cracks open, the hatchling does in fact have a miniscule residual scar where the cord was.

I doubt it falls off, the sources I looked up say that the whole yolk sac goes inside the bird's body.

You are right about the yolk sac! http://msucares.com/poultry/reproductions/poultry_chicks_embryo.html - However, it says that when they are born some residual umbilical cord tissue is still attached to the chick.  http://www.justcockatiels.net/assist-hatches.html  There are sometimes problems with the yolk sac being absorbed as well, so this could be related.

The first sentence is a fragment and doesn't make any sense. If you remove the parenthetical expressions, it reads: "All animals that develop in this way, whether they are oviparous or viviparous." Did you mean to say more?

How obnoxious of me.  'That' was removed.


text:
Why are women more susceptible to radiation?
The answer to this question on the Space.SE indicates women are more susceptible to radiation in space than men.

Why is this the case? Is it merely that women have less muscle mass (which being more dense than fat) and therefore may receive a greater dose when exposed?

It's actually because of the greater risk "from breast, ovarian, and uterine cancers" (article).  There's a more scientific write-up here, and while I don't have access the abstract implies that a more rigorous update of the exposure criteria upheld sex differences.  From a more terrestrial perspective, The Nuclear Information and Resource Service (nirs.org) has this rather incensed piece on the issue.  They cite a 2006 NAS report which

finds that harm to women (cancer) is 50% higher than the comparable harm to men from radiation doses that fall within the legal limit to the public over a lifetime.

Basically, it looks like females are more likely to get cancer from radiation, and once they do, those cancers are more likely to cause more harm.  According to the executive summary of NASA's 2014 in-depth report:

[A] 45-year-old man has a 344-day limit versus a 187-day limit for a 45-year-old woman, due to radiation exposures on the space station that would be typical at the time of solar maximum.

The effect of body size, however, could be the opposite.  Taller women get more cancer, with that study showing a 16% increase in incidence for every 10cm (4in) height increase.  That increase, however, is among certain types, such as melanomas, and not the above-mentioned "breast, ovarian, and uterine cancers."  Males, being taller, could therefore get more cancer overall; it turns out males usually die more from most cancers, just not (obviously) "breast, ovarian, and uterine cancers."


text:
What difference does it make in the organism's physiology/metabolism whether oxygen binds reversibly or not?
A follow-up to How does hemoglobin-free blood transport oxygen?
I'm unsure about the use of physiology/metabolism in the title there. The question in mind is whether this reversible binding makes an organism slower, or faster; perhaps more capable of surviving in rarefied atmosphere.
EDIT:
I apologize that my comment made it appear this question is only about the Icefish; it is not. There are still other species (for instance, molluscs, and arachnids) which acquire oxygen by means other than haemoglobin.

I'd love to answer this question, but I don't really understand it. If you are referring to oxygen binding by a carrier protein such as hemoglobin, then the binding has to be reversible otherwise the protein wouldn't be able to deliver oxygen to respiring tissues.

@AlanBoyd: The answer in the linked question indicates that species the binding is not reversible in Icefish; perhaps other species too. I'm curious about the nature of oxygen binding (reversible or otherwise) does it improve the ability of blood to deliver oxygen/nutrients and in turn what effect that has on the organism's physiology. Could it have evolved to enable the creature to survive adverse environment - as in the case of ice-fish?

The classic example of a hemoglobin adaptation to high altitude is found in the case of the bar-headed goose, Anser indicus.
This bird undertakes very high altitude migratory flight, crossing the Himalaya. It has a number of physiological adaptations that allow this, but it also has a novel form of hemoglobin with an unusually high affinity for O2. A single mutation changes the co-operative oxygen-binding behaviour of the haemoglobin molecule. In terms of the diagram in jello's answer, this shifts the binding curve to the left (i.e. toward that of fetal haemoglobin). This, in turn, means that the molecule binds more oxygen in the lungs, but it also means that it doesn't release the oxygen as readily in the peripheral tissues. On balance the former effect dominates and the efficiency of oxygen delivery is improved.

I think I see where you are coming from.  There is a misunderstanding here.
Ice-fish have relatively lost their hemoglobin gene over time because they have adapted such a slow metabolism in the cold water where the oxygen is richer (oxygen content in cold water is higher).  The don't need any binding of oxygen to a carrier protein like hemoglobin because enough oxygen diffuses in from the water for the needs of their tissue.
There is no binding - reversible or irreversible in their blood - that would imply that the oxygen is binding to a protein like hemoglobin or hemocyanin, which the fish does not have.   The oxygen is just diffusing into the fish from the water around it.  The circulatory system is helping by flushing the system out and keeping everything fresh as well.

Just to expand slightly on this answer, for clarity, the oxygen is diffusing into the blood at the gills, and diffusing out of the blood into the peripheral tissues where it is used for respiration. The blood and circulatory system of the icefish is performing the usual function, it just does it without an oxygen-binding protein.

@AlanBoyd thanks for this.  its possible there is diffusion through the gut and the skin too - remember salamanders and most reptiles have some oxygen from their skin too.

I don't understand your question either, but my response is to the question in the title. Oxygen has low saturation in blood plasma, so humans require hemoglobin to serve as a transport protein. Oxygen must bind reversibly, otherwise it gets stuck to hemoglobin.
Humans actually have two proteins, hemoglobin and myoglobin. Hemoglobin (HbA) circulates in the blood, whereas myoglobin is in the muscles. Myoglobin (Mb) has a higher affinity for oxygen than hemoglobin (see image). This makes sense, because the hemoglobin in the blood must unload oxygen at the muscles, and myoglobin must bind it. Hemoglobin's affinity for oxygen is regulated by 2,3-BPG, pH, and [CO₂] to ensure that it can unload oxygen at tissues.

(Curves to the left have higher affinity, meaning that they have a higher oxygen saturation for the same partial pressure of oxygen.)
Furthermore, humans have several types of hemoglobin. Fetal hemoglobin (HbF) has a higher affinity for oxygen than regular hemoglobin, ensuring that the fetus obtains the oxygen that it needs from the maternal blood.

Curious: If haemocyanin were to replace haemoglobin in a human body, would the person survive?

Ignoring the fact that hemocyanin is only in hemolymph and not red blood cells (as in humans), my guess would be no. Hemoglobin exhibits cooperativity, so that the binding of one oxygen molecule increases the affinity for other oxygen molecules. This leads to the sigmoidal oxygen saturation curve, allowing for more efficient dissociation of oxygen at target locations.


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Are genes associated with obesity selected for?
I've read that there are several SNPs associated with increased risk of clinical or morbid obesity. I was wondering if there is any evidence that these are under positive selection. Would you expect them to be so?
I guess I'm interested to know if they would previously offered a selective advantage and only recently, say in the post-war period in the West morbid obesity become a problem due to differences in the diet.
Related question:
How many, and how severe, are known single gene polymorphisms for obesity?

There are reasons beyond aesthetics why obesity is dangerous. Do not confuse obesity with "chubbiness", the latter can indeed be quite healthy and confer a selective advantage.

This is called the "Thrifty Gene Hypothesis" which was first used to explain why diabetes is so common. Basically it suggests that these alleles would have provided some kind of advantage, over the other possible alleles at that loci, until the environment changed. Then the environment changed and the allele became harmful. Environments are always changing and therefore favour different alleles (variant of a loci).
I suggest the genes linked to obesity in the modern world would, if tested on the old world populations would have been linked to being of a healthy weight. Further, those without it may have been skinnier and more likely to suffer from the disadvantages of being in such condition.
However, this paper present some counter arguments to the thrifty gene hypothesis. Speakman suggests that the genes responsible spread via genetic (allelic) drift rather than by positive selection. It is worth remembering that drift is very poor at spreading new mutations through large populations so there are also weaknesses to his arguments.
One example of a change in the favoured allele caused by an environmental shift is the DDT resistance gene in Drosophila which was present in the population at very low levels for a long period of time. As an aside, it possibly remained this way because it was subject to sexually antagonistic selection - beneficial to females whilst detrimental to males. It then spread through the population when DDT pesticides were used because it obviously became highly beneficial.  Many other examples of environmental change leading to different selection are around, this is just one off the top of my head. Another is the Galapagos Finches in a drought in the late 20th century.
HTH, if not please ask more and if it does then please accept it!

Hi, thanks for the answer and the explanation of the general theory explaining how this would happen.

I would think that genes favouring obesity nowadays in contexts of constant food abundance were in the past useful to store extra nutrients, when the food availability was irregular. One day you get something, you eat as much as you can of it and store the extra in the form of fat, and then you starve for some days, living on the fat you stored on the good day. I think I heard or read about such theories, but I have no reference for it.


text:
Evolution: One big population vs. many small populations
Let's say I want to evolve a bacterium that is resistant to an antibiotic. I want to do this by growing initially clonal populations of bacteria in presence of this antibiotic for a long time.
I have two options:

Make one 50 ml flask culture
Make ten 5 ml tube cultures

What are the comparative advantages and disadvantages of these two? Clearly, the ten culture version is better at probing the space of all possible resistance mechanisms. However, what about the rate of evolution? If I just want to get a resistant strain as fast as possible, which one should I use?
Note that "antibiotic" is just a proxy for any selective pressure, and "bacteria" is proxy for any organism. If possible, I think it will be interesting to address the effects of sexual vs. asexual reproduction in the organism that is being evolved.
There is already a question, How does rate of evolution/innovation scale with population size? that is very similar. I think mine is different, because it is not one small population vs. one big population, but one big population vs. many small populations. In other words, I am attempting to control for number of selection/mutation events, and focus only on the stratification of the total population.

Here are my thoughts. I might be wrong. Such process are mainly limited by the availability of mutations. In consequence, as long as the product of the selection differential and the population size is high enough, it does not really matter whether you split your populations or not.

If it's the same number of individuals in either set up then the rate of mutation will be the same, smaller populations are prone to drift so this could reduce the speed/quality of response in the smaller populations, but replicate populations will be requisite if you want to publish something, and interesting comparisons could be made between replicates (e.g. do they evolve different solutions to the same problem?) - my preference would therefore fall to many replicates

Note: This is not an area where I know the litterature well

Where are many counteracting processes to consider for this question. For instance, the rate of evolution will be affected by the rate of mutation, the distribution of positive and deleterious mutations, strength of selection, whether the fitness effects are small or large, if fitness effects depend on interactions between multiple mutations or single mutations with large effect, asexual vs. sexual populations, and processes such as genetic drift.
A recent review that is useful for your question is Lanfear et al (2014). They focus on how substitution rate is affected by effective population size, and go through both theoretical and empirical evidence. They conclude that in most cases, most mutations are deleterious, and that drift and selection are the most important effects in determining rates of evolution. They also state the effect of effective population size (Ne) is likely to depend if mutations are dominated by deleterious or advantagious mutations, and they expect the rate of evolution to be negatively correlated with Ne when deletious mutations dominate evolution and a positive correlation to Ne when advantagious mutations dominate.
A paper by Rozen et al (2008) indicates that while large populations are more effective in fixing mutations with large positive effects, small populations can be more effective in complex "rugged" adaptive landscapes.

While such determinism speeds adaptation on the smooth adaptive landscape represented by the simple environment, it can limit the ability of large populations from effectively exploring the underlying topography of rugged adaptive landscapes characterized by complex environments.

However, this does not deal directly with the rate of evolution, but mostly about attaining the highest possible fitness in a particular fitness landscape. Another interesting paper is Desai et al. (2007), but I haven't looked through this yet.  However, they find (for asexual bacteria) that the speed of adaptation scales less than linearly with population size, and similar results have also been found in studies from Lenski's group. Their interpretation is that evolution is driven by multiple concurrent mutations of small effect and not one-by-one fixation of single mutations (which would favour large populations more).
For your case of evolution of resistance, I think one crucial thing is if you expect resistance to be driven by a few single mutations or combinations of many mutations that interact (related to whether resistance is "easy" or "hard" to evolve). From what I understand, the first case should favour a single large population (since they will fix mutations for resistance more quickly), while the second case might favour many smaller populations (since you might get more effective exploration of combinations of mutations)
These are just a few starting points in a very large field, and I hope that you find them useful.

Very helpful! I especially appreciate the links to literature, thanks.

Nice answer (+1). As I said in my comment (and I might be wrong) I would tend to think that the difference between several small or one big population is totally negligible in this case because 1) $2\cdot N\cdot s$ will much large than $1$ anyway and 2) adaptation is mutations limited

With very large population sizes like this the effect of genetic drift goes to zero, which is greatly simplifying. I'm also assuming selection is very strong, so that fixation times are small, and that mutation rates and population size more or less cancels out, so there are a finite number of mutations and the selection space is relatively unexplored. If selection is weak everything takes longer, but I'm pretty sure the results are the same. There's greater exploration of alternatives, but that doesn't affect our thought experiment comparing population size.
In asexual populations: 10 cultures will give you ten answers to your selection criteria, one of which will be 'best'. One culture will give you the best solution a little bit later (larger populations take longer to reach fixation).
In sexual populations: One culture is better. The space of alleles is larger, and positive or conditionally positive mutations will be tested against more possible synergistic partners.
Consider that there are ten positive mutations split across your population. A sexual population in ten sub-populations has a tiny chance of getting all ten mutations into the same gene pool, but all ten sub-populations combined make it near-certainty that all ten mutations will make it into the same organism.
There's a limit to sexual population size above which evolution doesn't accelerate with additional individuals, because any additional mutations they bring to the table are eventually guaranteed to already exist in the gene pool. That limit is related to the genome size and mutation rate and probably other things, but for biological species it is enormous.

Both have its benefits and drawbacks.
The single big culture would have a bigger risk of contamination, but a bigger chance that the resistant mutated individuals are present, so in this case you would have a lower risk of complete extermination of your culture.
The smaller several cultures on the other hand will let you try several dosages of the antibiotic without fearing exterminating your culture. On the other hand each individual culture probably will have lower diversification, so lowers the chance of new strains.

RE the first segment of your answer, @superbest is using clonal populations as a base so this is not true in this case. There would be no standing genetic variance in the population(s) regardless of the population size, all resistance would have to come via new mutation. If the meta populations are of equal size (e.g. one population of $N$ individuals or 10 populations of $1/10N$) then there is no difference between the expected number of mutations between the two alternatives.

While you are correct and make valid points, in retrospect I realize that I failed to adequately specify that I am interested in the biology, not the methodology. As such I neglect contamination risk, and apply the same conditions to all cultures. (this is more realistic, if you think of natural populations)


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Can botulinum toxin be grown or kept from denaturing in an UNWRAPPED 50 pound hay bale?
Botulinum toxin is the neurotoxin protein created when botulism spores grow. The requirements for growth and/or for keeping the toxin from denaturing would seem to be very difficult to create in bale of hay.
There are well documented incidents of botulism in horses who are eating hay, all the references I found were centered around hay in large plastic wrapped bales.
I have been involved in an event where the presumed DX is botulism secondary to ingestion from hay from last year.  In this case the hay is second cutting timothy hay (making it 6 plus months old), in rectangular 50 pound (22 kg) bales that are not wrapped, have been barn kept, and when purchased from the vendor where stacked in rows 4 feet wide, by 6 feet (2 meters) high. The bale then spent more then a week on an shelf (chrome platted heavy wire) with good air circulation.
Three pet house rabbits appear to have been effected. with 2 dead and one recovering from a case of descending paralysis.  Several tests are underway, but my understanding is that it may be difficult to conclusively show either the botulism in the rabbits, or significant presence of 'botulinum toxin' or 'clostridium botulinum' in the hay (samples from the mangers of effected animals are being tested).
Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria?
Note
If there is an awareness of a plant based neurotoxin that would cause similar symptoms that may be growing in the hay field please offer that in an answer at Gardnening.

It's been a long time since I knew the ins and outs of botulinum toxin, but I do seem to recall that it's pretty resilient. Botulism is pretty distinct as far as symptom progression. I'll see if I can do more research and return.

@MCM, thanks it would be really great if you could shed some light on this.

As an addendum to Spinorial's answer, and after some research, the Center for Food Security and Public Health specifically lists hay / grass / decaying vegetable matter as a potential source for C. botulinum growth in their (very informative) Botulism PDF.

All species of Clostridium can produce spores, dormant
  forms  of  the  organism  that  are  highly  resistant  to
  disinfectants,  heat  and  environmental  conditions  that  kill
  vegetative  cells. These  spores  can  survive  for many  years
  until  favorable  conditions  allow  them  to  germinate  and
  grow. C. botulinum spores are common in the environment...
  ...
  Different  strains  or  groups  of  C.  botulinum  may  have
  somewhat  different  requirements. For  instance,  the  acidity
  necessary  to  inhibit C. botulinum  type C strains  is reported
  to be pH 5.1 to 5.6, but other organisms can survive a lower
  pH. Each group also has an optimal, minimal and maximal
  temperature  for  growth.  For  example,  some  group  II
  organisms  may  be  able  to  grow  in  foods  at  refrigeration
  temperatures  (3-4°C/ 37-39°F), but group  I organisms  and
  type  C  toxin-producing  strains  are  inhibited.  Because  C.
  botulinum  does  not  compete  well  with  other
  microorganisms,  growth  is  more  likely  to  occur  if  other
  bacteria  and  molds  have  been  killed  or  inhibited.  C.
  botulinum  spores  can  survive  cooking  and  some  food-
  processing  conditions  that  kill  vegetative  cells,  then
  germinate and grow in the cooked food.

As for your question...

Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria?

Could the toxin survive? Probably. The toxin itself isn't particularly hearty, BUT...
Could the spores survive (and go on to create the toxin)? Definitely. The spores survive direct heating/boiling, very low pH environments, and desiccation. For instance, botulism from canned foods can occur from eating the food (and toxin) directly - but you're supposed to throw it out if it look suspicious because even if you cook it and inactivate the toxin, the spores are still present after cooking. The spores can find anaerobic environments inside the body and germinate, then produce toxin afterwards.

Clostridium botulinum toxin is present ubiquitously in soil. As such it is more than plausible that hay bails, which come into contact with soil can and I should expect almost probably will be infected with these bacteria. However it is not the mere presence of the bacteria itself which causes poisoning, it is the toxins they produce when the appropriate conditions are met. These toxins are produced as a consequence of spore formation.
Traditionally in human cases, the presence of toxins has been linked to home canned foods, where there is an anaerobic environment with a ph < 4.5 (http://cid.oxfordjournals.org/content/41/8/1167.full). It is conceivable that such an anaerobic environment exists within a hay bail (even if not wrapped). The following site from the ontario minestry agriculture and food (http://www.omafra.gov.on.ca/english/livestock/horses/facts/info_haylage.htm) suggest that the pH certain methods of hay bailing have pH < 5. This would seemingly confirm hay as potential source for botulinum toxins.
With regards to testing the hay for C. botulinum I would expect there to be a very high chance of finding this, due to soil contamination, however this does not imply this was a definite source for poisoning. A more conclusive test would be for the toxin. So in summary it is logical to suggest that hay could be the toxin source, but this does not mean it was the source.

This is a very good answers, full of information.  I choose to award the bounty to @MCM as that answer more directly addresses the root question about the toxin surviving. Thank you both for your answers.


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Can dish soap really be used to kill ticks and fleas?
An answer at Pets suggested using dawn dish soap to kill fleas. I did a little looking around, and found several references supporting the idea.  Most of what I found was in 'selfhelp' and 'save a dime' type books and web sites. So while it seems to be a popular idea, I am unsure if it is an effective idea.
Is there any reliable science supporting the use of dish soap to kill fleas and/or ticks? If so what points in the life cycle would it be effective?  If it does work, how often would I need to use it to be relatively sure all the fleas/ticks have been through the appropriate life cycle and are dead?

I think completely submerging a flea in water, whether with dish soap or not (probably the soap could reduce air pockets in thick fur) would drown it, much like most terrestrial animals. However, fleas may be able to survive it for a protracted period (like cockroaches) so you may have to keep your pet in a bath for quite some time. I don't think eggs would drown, but the soap could disrupt their casing, poison them, or simply stop the adhesion and make them fall off hairs.

First part of the answer - Yes fleas (Siphonaptera) can be drowned. But not as easily as the internet would lead you to believe.
There are many claims on the internet (and printed works) expounding on how simple it is to drown fleas.  The best science I found so far on the topic is in Forensic Entomology: An Introduction By Dorothy Gennard; John Wiley & Sons, Apr 30, 2013; section 4.3 which reflects a 1985 work by Simpson K. (Journal of the New York Entomological Society 76: 253-265, not finding this online). Gennard is using the fleas present on a human body at death to determine how long the body had been submerged.  Findings -

A flea submerged for up to 12 hours will appear to dead, but can revive in about 60 minutes after being removed from the water
A flea submerged for 18 - 20 hours will appear to dead, but can revive in  4- 5 hours after being removed from the water
It takes 24 hours of full submersion to fatally drown a flea

Side note; lice (Phthiraptera) can be fatally drowned in about 12 hours.

Second part of the answer - Yes soap can facilitate the death of fleas in bathing
So far the best I have is Medical and Veterinary Entomology by Gary R. Mullen, Lance A. Durden Academic Press, Apr 22, 2009

This work suggests the process of washing the flea (and the pet) removes integumental waxes on the fleas body and they die from desiccation (dehydration).

More Research
I have been unable to find solid research specific to fleas (Siphonaptera) and soap (surfactants), so I had to reach in to the general insect works for answers.  There are a number of pesticides which include surfactants in their make up to increase effectiveness but these seem to be to an aid in the delivery of the pesticide not because the surfactant has any additional killing power.

a surfactant may affect the efficacy of an insecticide by its influence on wetting, spreading and run-off rather than by its influence on cuticular penetration

The Physiology of Insecta, Volume 6 edited by Morris Rockstein
There is some science suggesting soaps can help break down cell membranes but they seem to be most effective on soft bodied insects (which fleas are not)

Soaps... kill insects by disrupting the exoskeleton and breaking down cell membranes.  Soaps generally work best against small soft bodied insects such as aphids, scale crawlers, meatybugs, and young caterpillars as well as spider mites.

Destructive Turfgrass Insects: Biology, Diagnosis, and Control By Daniel A. Potter
Summary
There are multiple online reports of "drowning fleas" and killing them with soapy water.  After looking for the science there does not seem to be much support for these fatal claims. There is little doubt that giving your pet a soapy bath in the tub will help remove the fleas, they may even appear dead.  But in all likelihood these fleas are just waiting to dry out and be revived, hopefully in the city sewer.  If you bath your pet in the yard, and than let the dry pet in the yard again the next day the clean pet and clean revived fleas will likely reunite. Soapy water is more likely to facilitate removal of the comatose flea from the pet and carry it down the drain. So it is reasonable to have noticeable decrease in the flea population after a bath.  But excessive bathing has it's own risks and given the life cycle of a flea soapy baths alone are unlikely to be a final solution.

Though it's not important to the point you made, we can't forget the additional effects of some chemicals used in certain soaps.

You have to use Lemon Dawn specifically because they have Limonene and Linalool from Lemon essential oil. There are actually registered patents on these compounds for use in killing and repelling fleas and other insects.

Limonene: http://www.google.com/patents/US4379168
Linalool: https://www.google.com/patents/US4933371

Lemon oil paralyses and can kill the fleas. After the bath you have to comb the dog with a flea comb to remove the fleas, eggs and larva. Do this once a week and your dog should be flea free. Lemon also repels fleas, so it prevents re-infestation.

D-limonene, a citrus peel extract, is toxic to adult fleas; products with D-limonene plus linalool control both adults and larvae. DO NOT USE THESE PRODUCTS ON CATS, AS SOME CATS HAVE ADVERSE REACTIONS. Only use products on pets that are labeled for use on the animal
source(idl.entomology.cornell.edu)

I have added a reference that supports this claim.  Note that some reference suggest that there is more research required, and that if Limonene and Linalool are not used in combination, they are known to be ineffective.


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Why do squirrels have twitchy bushy tails?
Whenever I see a squirrel in the woods, it is always the big bushy tail flipping around that gets my attention first.  A pray animal with a big bushy flag calling attention to it's self seems to be counter survival, a big flag waving here I am, come eat me.

*Image from Wikisource
Video link, of tail twitching
Why do squirrels have twitchy bushy tails?
Edit to Clarify
Squirrels do not have a high reproduction rate, there are multiple difference between species but most seem to average about half a dozen young per year.. While a pair of rabbits can (though unlikely) create 1300 offspring in a year Wild rabbit and squirrels have similar coloring and predators.  There are of course multiple differences between rabbits and squirrels.  Given the difference in reproduction and a big wavy flag that says come eat me.  It seems that if there is a rabbit and a squirrel sitting on the forest floor eating breakfast, the one waving the flag is most likely to be seen and eaten.

Clicking on this post I was hopping to see a nice picture of a squirrel...I'm a little disappointed $\ddot \smile$. Also, you probably meant counter adaptive (or simply not adaptive) instead of counter evolutionary.

@Remi.b image and video link provided

Maybe female squirrels just like males with bushy tails? Squirrels are pretty agile and fast. I don't think slightly increased visibility due to a bushy tail is a serious disadvantage. Also, note the coloring of the tail in the picture. In case the squirrel has to hide its tail might even enhance camouflage.

The rabbit eating breakfast has a bright white tail it is waiving when running from predators. And long ears (though not fluffy). I don't really see a lot of difference between the breakfast mates visibility.

Tree jumping.
The obvious answer is that having a balancing ballast is incredibly handy for some of the death defying jumps squirrels perform. The tail is needed for that.
A big bushy tail might be a good counter to predation.
You make the assumption that an inconspicuous tail would be bad for predation. I would challenge that assumption, but I am making an educated guess so feel free to debate this.
Tail flagging in ground squirrels is used to deter predators and communicate vigilance. Perhaps something similar occurs in tree-dwelling squirrels too.
Rabbits have a short white tail which isn't particularly camouflaged. It helps to confuse the predator allowing the rabbit to make sharp turns that the predator cannot anticipate.
In the case of this big bushy "twitchy" tail (which like rabbits, some squirrel tails have white tips, like in your picture), a predator probably cannot see the body and importantly cannot see or is distracted from the footing and pacing of the squirrel. If you've ever seen a dog chase a squirrel, the squirrel is easily able to outmanoeuvre the dog long enough to make it safely to a tree, probably because the dog can't predict the squirrel's trajectory due to the distracting and writhing tail.
Let's say a predator did get its jaws or claws near the squirrel and tried to take a chunk. There is a good chance all the predator will grasp is a bunch of tail fur. The squirrel will probably be sore but will live to tell the tail. (I couldn't resist)

+1, just to have the honor of getting you up to 3k ;-) (and of course for your nice answer)


text:
What is the mass of a pigeon tail feather?
There is question at Space.SE If I drop a feather from orbit, would it burn up or “hit” the ground? there is an attempt to answer the question, but the mass of pigeon tail feather and possibly the drag coefficient is required to complete the answer.
I have looked around on the web and if there is an answer it is not jumping out at me.
What is the mass & drag coefficient of a pigeon tail feather?

An African or European pigeon?

@terdon - oddly enough, the same question was asked in a comment in the question that gave rise to this one.

I just weighed a pigeon tail feather (~10 cm) long. The mass was 0.05 g. Although all tail feathers are not equal in length (and all pigeons are not equal in size), this is probably a good approximation.
Measuring the drag coefficient is going to be very challenging, because it will vary with the orientation of the oncoming airflow. A feather falling with its broad surface (in this feather ~1.2 cm in chord width) perpendicular to the flow will have a much high drag coefficient than a feather falling with the broad surface parallel to flow.

Heh, nothing like the old fashioned empirical approach. I would expect the feather to orient itself with the pointy bit downwards though, it should be relatively standard.

@terdon such alignment, however, will only happen after the feather hits the atmosphere and survives the initial onslaught of unsuspecting air molecules. The orientation is uniformly arbitrary before the feather touches the atmosphere.

@JanDvorak yes, but we only care about the orientation after it hits the atmosphere. Obviously, there will be no drag coefficient in vacuum. I am guessing that as soon as it hits the atmosphere, the drag will orient it thusly.

Dropping most feathers (certainly primaries and body coverts, anything else should be in between) actually leads to them falling in a fluttering motion, rather than pointy-end first.  Pointy-end first is unstable (c.f. rocketry etc., or ask at physics.se)  Try it and see, it's also great for entertaining a cat.  A sheet of paper will often do the same.

@ChrisH I think (no idea really) that pigeon feathers, being relatively large (I'm thinking of entire plumes here, not tiny fluffy ones) would orient themselves pointy end down because of the extra weight of the plume. I may well be wrong though.

@terdon, in my experience it's not guaranteed even with the larger, stiffer feathers.  If you drop them shaft first they may keep going that way but dropped on any other angle they flutter and fall slowly.  The thing is that there isn't much extra weight because it's hollow.

@terdon I think it will flutter regardless, seeing as it is curved slightly.


text:
How does mineral oil kill a cockroach?
A recent post at a sister site Best field remedy for small cockroach in the ear has an answer that says

A few drops of baby oil (light nontoxic mineral oil) to suffocate the cockroach then tweezers to carefully remove it once dead and motionless.

This seemed unlikely to me, in the given scenario I suspected the baby oil had an additive. Per this link "some roaches can go up to 40 minutes without breathing" further suggesting suffocation was not the cause of roaches lack of motion.
I have done some more research and it appears this does actually work as described.

Doctors Settle Cockroach-In-The-Ear Controversy
The proper way to remove a cockroach from someone’s ear, it seems, has been the subject of little-publicized disagreement. The time-honored method is to drop some mineral oil in the ear, then try to pull the little critter out. A newer, competing technology is to squirt it with lidocaine, an anesthetic, to make it bug out on its own. Source

Both solutions above were ultimately successful. They found the lidocaine more effective.
Lidocaine does have draw backs as outlined in this article

Cantrell removed the dead roach with a set of alligator forceps, but the patient complained of dizziness for five hours after leaving the hospital.
"It is known that topical anesthetic agents entering the middle-ear cavity can be absorbed by the oval and round windows and cause vertigo," he said. The oval and round windows are parts of the middle ear used to transmit sound. Source

Putting aside which is the more appropriate choice. I just want to know how the mineral oil kills a roach quickly when it normally takes up to 40 minutes to sufficat one.
NOTE: Roach toxicity of Mint Oil is a completely different subject. (PDF)

Are you sure the cockroach died from the oil?

@StrongBad the references i read suggest they die from the oil.  There seems little question that at least they are rendered immobile within a few seconds to minutes of oil application.  If they come back to life like fleas do after drowning is not mentioned in anything I read. An answer supplying the mechanism of how the oil works on the roach should provide they answer to your question.

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


text:
Why are things conscious?
I've been referred to here from https://philosophy.stackexchange.com/questions/8052/why-are-things-conscious. Could you guys help out? Here's the question:
What is the reason for animals or more general entities being conscious? How did this evolve? What is the advantage?
I'm aware of ideas that consciousness is merely a illusion, however I find them less than convincing. The counter-argument would follow the line "if consciousness is an illusion, who has the illusion and more importantly why?". Additionally I believe that consciousness is a bare empirical fact. Even more, it is the basis for empirical thought. That "consciousness is an illusion" is not a good idea has been discussed by e.g. Searle (a video can be found here http://www.youtube.com/watch?v=yCii726A4Jc)
So what are good explanatory models for consciousness?

What is the operational definition of consciousness you are using? I believe it is a very vague and often ill-defined term that generally leads to unproductive discussions.

Look up Gazzaniga's left brain interpretor idea on google.

There are two very different questions here i) Why are things conscious and ii) What are some good models for consciousness. Could you narrow this down?

Actually, my first urge was to say, things are not conscious, otherwise I would not call them a "thing" anymore. But I guess that's more a question for the SE site this actually came from.

Because man was made in the image of God.

@Memming My working definition for consciousness is that for this question it is related to the experience of qualia, the mental images we form and experience day by day.

@terdon I suppose I'm mostly looking for an answer to the question: What is a good explanatory model for animals being conscious?

The thing is that consciousness is very poorly defined. Are ants conscious? Are amoebas? How about deer?

@terdon we should ask people who know about deer, ants and amoebas. However, I would guess that consciousness is a gradual thing rather than an on/off switch. So the consciousness of ants might be fairly faint compared to the consciousness of deer or you and me. I don't necessarily think that this poses a problem in finding a solution to the question.

Well, that's the thing, "consciousness" is a very vague and human-centric term. How can we know if other animals posses it? How do you define it? Where do you draw the line?

How can you know that I have it? I think that this is something you would assume based on a combination of behavior and similarity. I give somewhat coherent replies to your comments, I am anatomically somewhat similar to you (I have a brain) and so on. The same argument would go for deer and other animals. Having said that, I think that nobody would argue that the actual phenomenon is not real though (forget behaviorism). So it's more about finding a way to tackle the problem.

May I ask the person who downvoted me what the reason was?

Disclaimer: there is a very large amount of literature on the subject and I am in no way expert enough to properly review it here.
In any case, here's a few papers that review the issue and may serve as a basis to look up other references
Evolution of consciousness: phylogeny, ontogeny, and emergence from general anesthesia - Mashour and Alkire, PNAS 2013

We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution.
  [...]
  The distinction between phenomenal and access consciousness was noted, but phenomenal consciousness itself reflects the dissociable neurobiologica processes of awareness and arousal. Awareness refers to the content of consciousness (red apple vs. blue sky), whereas arousal refers to brain activation and level-of-consciousness (alert vs. drowsy vs. asleep vs. anesthetized). A number of current theories about consciousness propose that the cortex is the primary site containing the neural correlates of awareness, whereas midline subcortical brain structures provide ascending arousal influences to the cortex

This is also reviewed in this paper:
Subjective experience is probably not limited to humans: the evidence from neurobiology and behavior. - Baars, Conscious Cogn., 2005

Thus consciousness is not a metaphysical absolute, but a scientific construct like any other. In humans, the standard behavioral index of conscious cognition is accurate or verifiable report. It has been used scientifically since the beginning of psychophysics in the 1820s. Accurate report is highly reliable, but of course it is subject to limitations like any other empirical measure (Baars, 1988).
  [...]
  In humans the thalamus and cortex are crucial for supporting the contents of consciousness (Edelman & Tononi, 2000). Thalamus is often considered to be an extension of cortex, an added sandwich of interacting layers that controls most traffic to and from cortex. Local damage to cortical sensory regions, like the fusiform gyrus for face perception, results in a loss of conscious knowledge about faces but not about other visual features like color, location, or size. If the intralaminar nuclei of the thalamus are lesioned bilaterally, the conscious state is lost. By comparison, large lesions to cerebellum, basal ganglia, and spinal cord do not impair either conscious contents or state. Cerebellar damage can cause paralysis but not loss of consciousness. Lesion evidence on these points is supported by stimulation experiments using electrodes, transcranial magnetic stimulation (TMS), and microdialysis. It is also reflected in functional brain imaging. The evidence is therefore very strong that the T-C system supports consciousness. That is why many neuroscientists consider the T-C system to be the “seat” of conscious experience, and have done so for at least a century.

Again, citing from the first paper:

The recent experiments with general anesthesia in humans suggest that phylogenetically ancient structures in the brainstem and diencephalon—with only limited neocortical involvement—are sufficient to support primitive consciousness. Where, then, does consciousness arise on the evolutionary timeline? One might be tempted to conclude that consciousness commenced as our mammalian ancestors evolved just beyond reptiles and their predominantly subcortical brains. However, paleontological findings suggest that the synapsid line that gave rise to mammals and the sauropsid line that gave rise to reptiles and birds both diverged from the primitive anapsid line at a single point ~315 million years ago. Furthermore, there is significant evidence that avian species are capable of higher cognition and even consciousness itself. For example, birds demonstrate evidence of explicit episodic recall (i.e., conscious memory of an event) and theory of mind (i.e., attribution of subjective mental events to another being). Thus, it would be misguided to try to identify a single point at which consciousness emerged because evidence suggests that consciousness evolved along two independent lineages.

While it's still a very philosophical question, and neuroscience is not my speciality, I think that selfconscious comes from the integration of several informational sources.
Our brain has maps, that's a fact. We have maps to locate sensorial signals (in fact, all our senses are neural maps representations), to locate our muscles and we even have secondary maps that allow to compare the movements we desire to make and the movements we are actually making. The integration of all of this maps leads to a pretty accurate idea of ourself, and that's critical for selfconciousness.
Furthermore, our brains uses our senses to create images of our immediate sorroundings. They also need to locate other important places (for instance, even if you're at home you would proably have a mental idea of how far your workplace is). Moreover, we have a psicological idea of time wich places ourselfes in a present after a bunch of events that have already happened andd before a set of possible events that we have modelized or predicted with the information from the past. All of this creates an idea of our place in the world.
By combining this two ideas we have a global mental model of our own state, our own desires, our own characteristics, etc... placed in an mental image of the world based in our previous experience. Of course memories and thoughts would have its place, too, but they are more complicated to explain briefly.
Transversely, I don't think that computers would develop selfconciousness by its own even if someday they have more computational power than the brain. First, a computer doesn't need an idea of itself as a phisical being, unless it is programmed to do so (a robot would probably have it, thought). Second, the inner logical architecture of computers and brains is quite different, being maybe the lack of biologycal instincts the most relevant difference. Of course all of this should be programmable. My point is that is quite unlikely that it appears by itself and that a selfconcious computer is a pretty unpractical device.

+1 @Miguel (although I'm not signed up here) for actually posting an answer and a good one too. Besides this, I'm still wondering how neural maps are able to lead to the experiences we have. I simply can't see the mechanism there. That is besides stating that this is what neural maps do. To me this is "spooky action at a distance", i.e. not a real explanation. And I won't believe that a PC will have actual consciousness rather than simulated one until I see very solid proof for it. But an honest thanks still for the answer. There are really good points in there.

Neuroscience is my specialty.  What we call consciousness is thought to be an evolutionary elaboration of a property of cells called "irritability", which is the cell's ability to respond to signals from its environment.  There are many manifestations of this: chemicals binding to protein receptors, light interacting with proteins (as in photosynthesis), mechanical forces causing cell movement, bacterial chemo-taxis, and the list goes on.
The analogy is like this.  What we call eating and elimination are analogous to cell metabolism.  As a whole organism we must eat to replenish the body, and eliminate the waste produced. A single cell must also absorb nutrients to maintain itself and eliminate the waste products.
So, it is like a fractal.  The same functions displayed by individual cells also manifest at the level of the whole organism. So, as the GI tract is the organ analogous to cell metabolism, the nervous system is the organ analogous to cell irritability.  One could imagine that what we experience as our personal consciousness is in fact like taking an integral over the irritability of all the cells in our nervous system.  Many people focus on the neurons, but all the cells in the brain contribute to the brain's function.
Now, this form of explanation is not really an explanation as much as it is a description of our biology.  The obvious question arises: why are cells irritable? Because, irritability is basically the individual consciousness of an individual cell.  Well, one then realizes that the response properties of cells to stimuli come from the action of the molecules and forces that make up the cell. The immediate forces are non-covalent interactions, mainly poorly understood even in terms of physics, such as forms of adhesion (consider Velcro or glue). These are emergent properties that stem from the assemblage of molecules of which cells are composed.
But let us grant that physicists eventually come to understand such "derived" forces in terms of the elementary four forces of the universe: electromagnetism, gravity, strong and weak nuclear.  Then, it is clear that there is a potential contained in these forces to combine in ways that cause complex molecular assemblies that self-organize and display irritability.
Thus, the issue of consciousness presumably links back to somehow being an inherent emergent property of the forces of nature.
Again, this is all relatively uncontroversial, but building such a chain of explanation is not really an explanation as much as just being a description of how things are organized in the world.  And I think it is clear to any thinking person that a description of something is not the same as an explanation of something.
So, if you follow this far, then you can appreciate why the Greeks thought that Atlas, who held up the world, stood on the back of a tortoise, and this tortoise was on top of another tortoise who was on top of another tortoise, all the way to infinity.
We have simply replaced Atlas and the tortoises with language of modern science.  It is still an infinite regress.  The short answer to "why are things conscious" is that it seems to be a property of the universe to display consciousness.
Now, there is one great man who thought about this problem and constructed what I consider the best explanation.  This was Gottfried Leibniz, the man who invented calculus.  Leibniz invented the idea of a "monad", and he considered monads as the basic units, the atoms, in the sense of being the indivisible units of reality.  The monad, as an atom, is pure consciousness.  So, Leibniz came to the conclusion that the reason there is consciousness is because consciousness is the fundamental building block of reality.
Monads are what everything is made of: us, cells, atoms, quarks, electrons, etc.  These are all different forms of monads.  According to Leibniz, they are all different forms of consciousness, and they combine in fractal patterns to make forms of consciousness within forms of consciousness within forms of consciousness.  And this pattern goes in both directions from the infinitely small to the infinitely large.  According to this idea, just because something does not seem to be conscious in the same form we are conscious does not mean it is not conscious.
This is how Leibniz solved what is called the "mind body problem", which is really the heading under which your question falls.
If one wishes merely for intellectual understanding of the nature of our consciousness, it is my opinion that Leibniz' ideas are the best available.
If you wish to go beyond mere intellectual understand to a deeper level of awareness of these issues, then I suggest you look up and study the works of a writer named Patanjali.

Could you please link to some literature at this regard? I never heard about "cell irritability" in the context of the nervous system, or when speaking of multicellular species for that matters. I think that for the scope of this site a proper neuroscience answer would have to be preferred to a phylosophical answer (Leibniz is all nice and good, but he was not what I would call a neuroscientist).


text:
How deep in the soil can a seed be placed and still develop into a plant/tree?
The selected answer to How does a plant grow before photosynthesis is possible? indicates that a sprout grows beneath the soil using the food stored within the seed.
Does this limited ready food place a restriction upon the depth to which a seed may be placed and still develop into a plant? What depth will be best applicable for a given plant/tree seed? Is there a mathematical relationship known?

TL;DR 1) yes, 2) depends on species, soil, climate, 3) yes

@David: Could you flesh out the mathematic relationship please? Is the math relationship universal, or species/phylum/order specific?

there is no single mathematical relationship, but I have tried to provide a general answer please let @richard or I know if you have further questions

The general mathematical relationship requires an allometric equation. There are not as many for seedlings as there are for mature trees (but see the answer by @Richard-smith for a specific example). But lets start with a basic assumption that the emerging seedling will be a very tall cone (tall = high h to r ratio).
The volume of a cone is:

$V = \frac{1}{3} \pi r^2h$

Then we need to know the density of the seedling to figure out how much carbon a seedling of height h would require. Lets say that the density is 1.5 g/cc (excluding water).
Then, assume that the biomass is 1/2 carbon (a fairly reasonable assumption).
To figure out how tall a seed could grow given carbon reserves, it would be necessary to determine the amount of carbon in storage in the seed. Say there were 5 grams. There will be a carbon cost of reallocating this to growth, say 50%. So, for a seed that has 5g of carbon, its total volume might be calculated as:
 (5g * 50% growth respiration)/(50% C content of biomass) * 1.5 g/cc = 7.5 cc

assuming that the seedling will have a radius of 0.2 cm, the height could be calculated as:

$h = \frac{V}{(3 \pi * 0.2^2)}
    = \frac{V}{0.38}$
          = 20 cm (for V = 7.5)

Note: this is just a very quick "back of the envelope" calculation with many assumptions. C is 50% of plant biomass is pretty close (the actually number is closer to 48%). The growth respiration cost is a very rough estimate, and will vary with nitrogen content of the tissue, soil temperature, and etc.. The plant will likely need carbon left to build a leaf, and another resource may be limiting.

Excellent derivation from principles, nice answer

@RichardSmith Thanks for looking it over. I just wanted to make sure I didn't miss anything obvious.

To answer your specific questions...
Does nutrient availability limit emergence depth?
Yes, the size of the nutrient store in the seed does impose a theoretical limit on the maximum depth at which seed germination and emergence can take place.
What is the best depth for a given species?
The specific depth which gives best germination for any given species is very unlikely to be the maximum depth at which seeds of that species can germinate. This is because other factors also impose limits on germination depth.
Probably the most important other factor is light - most seeds require the perception of red light in order to trigger germination. For most species then, you are unlikely to find seeds germinating and successfully emerging from depths greater than the penetrance of light.
Another important factor in some latitudes is temperature - many seeds (from 26 families) use dormancy as a way of preventing germination in the wrong seasonal conditions. In species where temperature serves as a cue to alleviate dormancy, there will be a maximum depth at which a given seed can detect the temperature fluctuations at the surface. Beyond a certain depth, surface temperature changes will not perceptibly affect local temperature.
If you ever need to find out the best depth of germination for a given species, many can be found on google, or failing that it is trivial to perform a simple experiment.
Is there a mathematical relationship?
There is a general mathematical relationship, an allometric relationship (i.e. relating size to another trait), between seed size and maximum depth of emergence, described by Bond et al. (1999):

where:
dmax = maximum depth of emergencew = seed weightc = a constant which varies with phylogeny and environmental conditions.
Many species however will not submit to this equation. For example some large-seeded species (incl. coconut, coco-de-mer, avocado), have large seeds because they may need to enable long-distance growth along the ground in order to locate optimum growth conditions. Seeds of these species will therefore not conform to the depth-size relationship above.
Reference

 Bond WJ, Honig M, Maze KE. 1999. Seed size and seedling emergence: an allometric relationship and some ecological implications. Oecologia 120: 132–136.

nice answer. I'd appreciate your opinion of mine.

Generally a rule of thumb in gardening is to plant the seed 1-2 times as deep as the seed is big. a pea can go 2 cm, a poppy can go 2mm.
The starch of the seed is converted into sugars, which causes osmotic absorption of water by the new plant cells, and they have about 100-200kpa of upwards turgic pressure maximum, that's equivalent to more than 50 meters of lithospheric pressure.
So it depends on the size of the seed, the main inhibitor is the energy needed to create the hydrostatic pressure in the stem to maintain pressure and cell growth for the given distance.
In dry clay soil which is like concrete, chances are that the plant will not be able to go up, but in sandy soil you can expect some seeds to pierce many meters of sand, unless there is zero light.