You are correct, burning carbohydrate produces various combinations of C, CO and CO2, plus H2O. More importantly, the process of biological respiration takes sugar and effectively "burns" it in a series of controlled steps, but resulting in waste CO2, and water. The CO2 is literally breathed out, replenishing what the plants used to make the carbohydrates. The water is produced using oxygen gas as the final acceptor in the electron transport chain, so those molecules enter the population of other waters in our body, to be used like any other, or may be Incorporated directly into other molecules. Either way, it takes the place of one water molecule that would have been brought from the outside to fulfil the same function.

In essence, oxidative respiration is the biological mirror image of photosynthesis, in that each feeds the other in a beautiful meta-circle.

(posted in Plants & Fungi)

It may simply be an accident, with no purpose. It could be that the pollen grains you saw were from a different plant and so could not fertilise the flower. It is also possible that the pollen or the flower itself could be infertile, perhaps due to a pesticide or a growth abnormality.

Hi Carrie, those are good scores, and you certainly need to have your wits about you to be a scientist. I don't think that "qualify" is really a good term. I have never had to supply my IQ for any part of university education, or at any job since. To be a professional scientist you need a graduate degree at least, generally a PhD if you want to work as an academic. The only thing your GPA is really good for is university entrance to get those degrees, which is where the real work begins!

In my experience less attention is paid to IQ scores than to demonstrating hard work, dedication to excellence and perhaps above all the ability to turn research into peer reviewed publications.

Good luck, I'm sure you will be an excellent Paleontologist!

I'm not sure exactly what your question is here, but I'm pretty sure that no one could answer many questions about infections in creatures that ancient. I think you are asking if the evolution of warm-blooded creatures somehow made their cold-blooded cousins more susceptable to infectious disease.

If I were to speak very generally,  I could say that while occasionally pathogens do cause mass sickness and even death, for the vast majority of the time pathogens and host organism are in a constant co-evolutionary stand-off where there is little or even no disease except for what we term "opportunistic" infections; open wounds, weakened host through hunger, impaired immune system. So to some extent we evolve in tandem with our diseases, called co-evolution.

One thing we can say is that pathogenic organisms are often quite specific, especially animal viruses, with only rare (but significant) examples of cross species transmission. Bacteria and fungi are less fussy for a place to live, but to grow optimally they need a fairly narrow temperature and humidity range. So, as a general rule, species of pathogen (be it virus, fungus or bacterium) that might infect an endothermic creature would be much less well suited to infecting another animal who lives at different temperature. My guess is that existence of one probably would not directly cause the other to have increased disease, except in exceptional circumstances.

Sorry I could not be more specific, you questions is very broad

Hi Tina,

Animals have eyes for a few different functions. One of the most basic is simply to tell light from dark, so that the animal can keep track of large changes to its environment. This doesn't require complicated eyes, just a patch of light-senstive cells is sufficient. Seastar (because they aren't actually fish!) eyes are very simple, in that they have no lens like our eyes do. They also work very slowly, meaning that they have to be able to look at something for a while to be able to see it, kind of like taking a long exposure with a camera. Seastar eyes are very poorly studied, and it is only recently that we have begun to understand how they use them. To find out some more, have a look at this article from Ed Yong, one of my favourite science bloggers.

http://phenomena.nationalgeographic.com … heir-arms/

Commensalism usually refers to two or more species that share living space or food source, where one gains some kind of benefit without affecting the fitness of the other. Mutualism refers to a beneficial relationship that two or more species get from living with each other, where both species gain benefits. Mutualism can be separated into facultative (optional) or obligate (necessary), and is sometimes alternatively called symbiosis. The question you must ask your self about the example of clown fish and anemones is: do both parties benefit, or only one? Does the fish simply gain a safe place to live or is there also a benefit to the anemone?

There isn't actually a sharp line dividing the two, and sometimes a case could be made for both! Have a look at the wikipedia article on mutualism, it outlines the issues fairly well.

http://en.wikipedia.org/wiki/Mutualism_%28biology%29

Hi There,

Your belly button is definitely not a hole! The belly button is basically a scar from where your unbilical vessels once entered your body in utero. The umbilical vessels travel between the placenta and the growing embryo.  Before birth, a baby receives all nutrition via these vessels, and one end interfaces directly with major vessels close to your heart. At birth, when the baby takes it's first breath, this vessel closes off via a sudden pressure change as the lungs work for the first time. After this point the umbilical vessels are no longer needed, so the bit outside the baby's tummy is tied and cut, forming your belly button. Once the internal vessels are no longer in use, they drain of blood and are allowed to atrophie into remnants by the new born's body and are no longer used for blood circulation.

(posted in Evolution)

Adaptive radiation is where an ancestral form adapts to multiple niches, resulting in many related populations with different life styles. I don't think that this can be used to describe humans. Yes we have spread all over the world, and there had been some superficial adaptation, such as skin colour or lung size, but I'm not sure it could be called adaptive radiation. We are still one species, we can all interbreed. Another way of looking at it is that with only a few exceptions most of humaity occupies the same basic niche, that of the dominant animal, the hunter and farmer. In general, we all like to live on the same kinds of land; where there is water, good soil and any natural resources we can exploit.

Each type of transgenic animal would need to be specifically evaluated, and that is a very broad question. Harmful in any manner? I suspect no more so than a contemporary non-GMO animal. A specific exception would be if the animal were engineered to produce a substance toxic to humans, which we then ate. I know of no such animal. I would be far more concerned about the routine use of antobiotics by farmers and the potential to raise antibiotic resistance pathogenic organisms.

Hi John, I'm afraid that no one knows the answer for sure. But, there are two ways of looking at possible explanations

First, it could be that a longer life was not necessary for survival. In fact, it could be a detriment as a longer life means more competition between parents and offspring. Also, a longer life is usually associated with slower breeding, which is a serious problem for future adaptation; if a population cannot breed fast enough to adapt to a new challenge, it will go extinct. Old animals dying out and allowing the next generation to take over is how evolution happens, so if you slow this process you slow evolution.

Second, it could be that it simply never happened by chance. Although evolution is not random, it can only work with what is available at the time, so it is possible that extended longevity was just never "discovered" in humans. For example, our mammalian physiology is very different from turtles or trees, meaning that the kind of longevity you are talking about may not even be possible.

Having said that, humans in industrialised nations have a life expectancy of about 2.5x the span of humans who lived 10,000 years ago! It could be said that the evolution of intelligence, which resulted in advances in science/medicine/engineering, has indirectly resulted in a huge gain in human life expectancy.

Well, I was perhaps being too generous with the definition of sex, meaning just the exchange of genetic material between contempoararies of the same species to create a new genetic combinations. Maybe lateral transfer is a more appropriate term, but I always equate it in my head to essentially the microbial version of sex. I may have used it in the wrong context there, so perhaps was unclear.

Hi Sami, science says that humans evolved from an earlier ape ancestor, which we share with chimpanzee, gorilla and neanderthals. Sex evolved well before gender, so gender probably co-evolved, meaning that there was no first; the male and female genders evolved together.

Hi Simon,

Bacteria have a double membrane, and the proton gradients are built up in the periplasm, the space between the membranes. This is exactly what happens in the mitochdrion, and indeed they are believed to have once been free living aerobic bacteria.

Yes, and I believe this has been done, though not without some contraversial failures. The resulting offspring is said to have "three biological parents", because they get maternal and paternal DNA just as you describe, but also the mitochondrial DNA from a third party, the egg donor.

Have a look here:

http://www.bbc.com/news/magazine-28986843

A great many questions! Too many to answer here.

Here are some links to start you off.

First, abiogenesis and the RNA world
http://exploringorigins.org/timeline.html
http://www.talkorigins.org/faqs/abioprob/

Evolution of complexity
http://en.wikipedia.org/wiki/Evolution_ … complexity
http://www.scientificamerican.com/artic … omplexity/

Questions regarding the evolution of genitals and sex have been asked before on this site:
http://www.askabiologist.org.uk/answers … p?id=10179
http://www.askabiologist.org.uk/answers … hp?id=4664
http://www.askabiologist.org.uk/answers … php?id=900

on the cambrian explosion specifically:
http://www.askabiologist.org.uk/answers … php?id=111

Forget the word "random". Mutation is random, but evolution doesn't happen until you get selection, which is definitely not random. To put it another way, evolution has elements of chance in it (called stochastic) but is over all a highly ordered process.

What came first "blood or heart"; That one is easy, blood. When you are very small you don't need a heart to pump fluid, it just kind of sloshes around inside and does a good enough job (look up hemocoel, and osmosis). When body sizes increased, osmosis isn't fast enough so you need a pump and much more efficient system (circulatory system).

Your digestive tract is virtually the first recognisable structure in the embryo that will become you. We have had a two-ended mouth/anus system for a long, long time, well before there were humans. There are some animals without an anus, and they discard wastes back out through their mouths.
http://en.wikipedia.org/wiki/Gastrulation


The question about the big bang is definitely not biology, so don't expect any expert answers here. However, your assumption that "something" came from "nothing" may not be correct. There may have been something before the universe, we just don't know what. Basically it's an open question:)

Hi Lian,

We know that mutation and selection leads to evolution because it can (and has been) conclusively demonstrated both in the lab under controlled conditions and in real-world field studies.

For example, development (ie natural selection in favour of) of antibiotic resistance in pathogenic mircobes can be directly linked to a mutation, or series of mutations. In the lab, the Lenski experiments on citrate metabolism illustrates the concept very well indeed.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937522/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430337/


In a more general sense, physical characteristics are the basis of selection (the "phenotype") and your genes (the "genotype") are the heritable basis of phenotype. There is variation in the genotype, which occurs naturally (think how many different types of human there are!) by accumulating mutations in individuals. Selection happens when the environment puts a bias on a particular kind of variation, favouring one over the other through greater success in breeding over all in a population. This results in an increase in the population of the favoured ones and decrease of less favoured or harmful variations. Subsequent generations have more of these favoured genes, and they also have a new set of variations, which can be re-selected again. Over many generations in this way, the population can change a great deal by this gradual biased selection. If you give it long enough, the changes can be MASSIVE, eventually producing all of the structures you mentioned; eyes, ears, etc.

Eyes are actually a great example, because it appears that eyes independently evolved multiple time in different animals through this same process of selection from variation. Tetrapods (like us humans) have one kind of eye, cephalopods (like squid) have a completely different kind, and arthropods (insects, spiders, crabs) have yet another different kind. In fact, virtually all animal groups have some kind of light-sensitive organ that could be called an eye-like structure. Each of these have entirely separate and in dependant evolutionary origins, produced by selection from variation over many, many generations.

One of the most convincing pieces of evidence for the validity of evolution by common descent I have personal experience with is ancestral enzyme reconstruction. Common descent is the notion that species diverge from a parent species, and our genes reflect that in both their similarities and differences with other species.

The idea is; if we build phylogenetic trees (a tool for figuring out possible patterns of evolution) of a particular family of enzyme proteins based on their genotype, it is possible to statistically infer the probable sequences of the ancestral enzymes by assuming common descent. And we are talking a divergence that happened up to 800 million years ago. The incredible part is that this approach does work, it can produce functional enzymes with different characteristics. If common descent were not true, I don't believe this approach would work nearly as well, if at all.

http://www.talkorigins.org/faqs/comdesc/
en.wikipedia.org/wiki/Phylogenetic_tree

Hi Simone,

When we look at our mammalian cousins, we can see all of the same organs as we have. Some are larger, some are smaller, occasionally some are missing and new ones added, but the basic body plan that humans have was evolved way, way before humans existed. I'm not sure about making them "better" in humans, in some cases they are decidedly worse. For example, we have a larger brain proportionally than most other animals which gives us good thinking-powers, but our vision is actually pretty poor compared to other animals, especially birds. Our sense of smell is also fairly poor compared to other mammals. A better way of thinking about it is that we have inherited an ancient body plan along side all mammals, and our circumstances have adapted it a bit to fit our niche.

(posted in Evolution)

Hi Simon, that is a very complicated question without a quick answer:) edit: Strictly speaking it isn't really a science question, but a philosophy question. I'll do my best to answer it, but it is important to recognise that some questions have lots of different potential answers when we have very little evidence to go on, and this represents only my view and not necessarily the scientific concensus on the likelihood of the universe being created by an intelligent designer.

Evolution does not predict how life began, it only deals with the processes that happen after self-replicating life has arisen. The step between life and non-life is called abiogenesis, but it isn't really a step. The line between chemistry and biochemistry is not sharp, it is very, very blurry. Only a degree of organisation and complexity separates the two. There is no magic elan or spirit which living things possess and inanimate things do not.

What we can say is that so far in all of the hypotheses and theories of science, the action of "god" has never been shown to be necessary to complete an explanation, and we therefore have no need for the god hypothesis. One of the stumbling blocks of formulating a god hypothesis of origins is the poorly defined nature of god. Without a definition, how can we hope to make definite statements on the nature or existence of god? But the main problem with it is that explanations that invoke a god are either infinite regressions or circular.

I'll explain what I mean.

edit: i deleted a paragraph about circular arguments because I did a terrible job at explaining! Sorry, I might try again in a another post:P

Now the infinite regression: Suppose that in a hypothetical world it is shown that natural selection and other naturalistic processes are not sufficient to account for all the complexity in the universe. This is often referred to as irreducible complexity, and also is kind of used in the fine tuning argument. Basically, IDers claim that an intelligent designer is the only explanation for the existence of complexity because beyond a certain threshold simple things cannot produce complex things. This does raise a new question though; if complexity must be created, what created god? This leads to an infinite series of creator gods, each creating the next. The escape from this logical trap is to claim that god is not complex but actually quite simple, which therefore means it could not have created the complexity it was being used to explain in the first place.

So in answer to your question, I don't think science makes it less likely that the universe was created by a supernatural being, because the likelihood of such a creation event has never been sufficiently defined to make such a probabilistic statement! How can we ever hope to do a meaningful comparison? All we have been shown is circular arguments, infinite regressions and faith-based convictions. Science is based on evidence, and there isn't any unambiguous evidence for a creator god.

That doesn't mean the question is settled for ever, there is always the possibility of new evidence changing what we know, and there are of course lots of people who disagree with what I've written above:)
Here are some links to start from so that you can reach your own conclusions.

http://www.talkorigins.org
http://en.wikipedia.org/wiki/Irreducible_complexity
http://en.wikipedia.org/wiki/Fine-tuned_Universe
http://biologos.org/questions/what-created-god
http://en.wikipedia.org/wiki/Teleological_argument

There is software that can analyse and quantify bands, it is often part of the gel dock photo software that takes the picture in the first place. Presence/absence can be empirically determined by looking at a background segment (ie no band) and defining a band as some minimum brightness above background.

It can also be acceptable to assess by eye. If this were me, I would look for a discrete band at the right size and try convince myself that it is not a gel artifact through smearing or just random staining inconsistancies. I may need to run the same sample twice, or load more on to the gel to be sure.

Having said all that, you really need to speak to your supervisor/boss or other senior members of your group to nail this technique down properly.

I have nothing to add, except to say that is an awesome looking bee. Good photo:)

For alignments and tree building ClustalX is the usual goto standard, though modern databasing software like Geneious has far outstripped those basic tools.

There are literally hundreds of online tools scattered throughout the web. Have a look at expasy, a catalog of tools with links. Fasta is a standard format and most tools accept it.

http://www.expasy.org/

Sleeping is basically a loss of consciousness, which is why you wake up and suddenly it's morning without experiencing all those hours in between.

Being awake is the polar opposite, ie you are conscious. Your question is a little unclear, but I think you are asking if you can induce a period of unconsciousness while simultaneously remaining awake. I don't believe that is possible, and they seem to be mutually exclusive states by definition, though sleep is an active area of research and there are grey areas such as sleep walking. There is one way to make what you describe happen while awake; fall asleep!

I'm not 100% sure on this, but focused concentration can seem to make time run faster, even if you are simply meditating. There are such things as hynogogic trances, sometimes attained through the use of drugs.

http://en.wikipedia.org/wiki/Hypnagogia

People who consume large quantities of alcohol can lose time while awake, thought I cannot recoment that!

In the process of sleep your brain (and body) is still doing things, it's just that you don't remember it. To get this effect while awake I suspect you would need strong drugs or epilepsy (or some other severe brain disorder/injury).

No, it isn't true that we evolved from bacteria.

The term "bacteria" is quite specific, just like "animal". While the current thinking is that all life evolved from a single-celled ancestor which may be superficially similar to bacteria, what we call bacteria today is the product of ~4 billion years of evolution from that single celled ancestor. So, we certainly did not evolve "from bacteria". Instead, bacteria (which is actually more accurately divided into two completely separate groups; archeobacteria and eubacteria) and us have a common ancestor which was probably single-celled. We can expect that the common ancestor is as different from us humans as it is from any given bacterium alive today.

Common decent is heavily implied by the common biological chemicals we use, namely DNA, RNA, lipids, sugars and amino acids. Also, we have conserved genes in common, in particular those around protein production and other basic molecular biology (e.g. the ribosome). This basic machinery is so much the same that human genes can be utilised by bacteria under the right circumstances, and the other way around can work too.

Having said all that, we don't know 100% that this view is the correct one, but all of the evidence points in that direction and at this point it would be very surprising to say the least if it were shown to be false.

(posted in Mammals)

Well, I am going to guess that your question is "can cats feel regret?".

It is very, very difficult to show objectively that non-human animals have emotions that are like our own. Between humans we can only perceive emotions as indirect things, like through tone of voice, body language and facial expression that we can only interpret correctly because of our shared biology and cultures, and even then we quite often get it wrong. In certain specific situations, like with domestic dogs, some of that interaction is learned, but how much of that is simply training, and do the reactions really correspond to anything recognisable as human-style emotions? Sometimes the inference seems obvious, like with a fear response, or just general excitement. On occasion I have seen dogs display what I would call guilt.

But when you see your cat doing something that apparently conveys an emotion you recognise as one you might have yourself, it does not follow that the animal has the corresponding emotion. An analogy is seeing a "smile" on a non-human animal. Is it happy? Threatened? Constipated?

This is especially true when it is something as complicated as regret for an action that hurt another. In attributing this human emotion on to your cat, you are making the asumption that it does in fact recognise you as a fellow creature with emotions of its own; in other words, can a cat meaningfully empathise with you to understand that through it's actions it caused you harm and thereby feel sorry it did so? If you have ever seen a cat playing with a bird it may lead you to think that cats cannot be empathetic in that way, because if they are then they can only be described as heartless, torturing killers without remorse or pity.

Males are generally bigger, with bigger bones, muscles and even brains. All organs are  larger on average. That's it, no mystery.

I think the best word to describe it is tentative. There is so very little direct evidence, but there are broad hints, like the RNA machine that is the ribosome, as well as experiments showing that such a world is possible at least in principle. So yes, intriguing and promising, but tentative at best. The main problem is that there is so little information about conditions on ancient earth, and even what info we do have is necessarily broad and general. The kind of chemistry needed to make an RNA world work requires are relatively specific set of conditions, and unless we can be more specific about the ancient earth, I fear these origins hypotheses will always be only tentative.

This website has a pretty good basic summary of the RNA world hypothesis.
http://exploringorigins.org/rna.html

This may or may not be relevant, but my younger sister had chronic nose bleeds. There was no clear cause, but there did seem to be a link between aspirin use (a blood thinner) and the bleeds. The suggestion was that the mucosal blood vessels were in some manner thin-walled or perhaps too close to the surface, and the combination of blood thinners with extra pressure (like energetic sneezing/swelling) compromised them and caused the bleeding.

No one knows for sure, but I think it is difficult to project human-style feelings on to another animals. Human feelings are typically conveyed by body language, facial features and language, each of which is quite human-specific. In our very closest non-human relatives, chimpanzee, we can justify equating particular identified emotions to those that we have because of our similarity. The further you get (and sharks are quite far removed from mammals) the more difficult it is to justify.

I think that it is pretty safe to say that sharks feel pain, but I'm not comfortable taking it much further than that. Even assuming that they do have analagous emotions or motivations, I feel that we would be unable to recognise equivalents in ourselves, aside from the basic pain/hunger/mating impulses that seem to be common to all animals.

(posted in Evolution)

Yes, you are failing to appreciate the effect long time scales can have. Even slight advantages, like partial camouflage, can go to fixation over long enough time scales. Of course, over those same time scales further mutation and selection occurs, resulting in a kind of feedback loop making the camouflage better and better adapted.

All organisms contain mutations that their parents didn't have, including you. These don't need to be beneficial to persist, just neutral, which is almost all of them. Benefit/detriment is of course contextual, so a mutation which is neutral or bad under one circumstance can become beneficial in another. In the case of camouflage, I can easily imagine how small variations in pelt/feather/skin colour and patterning can occur within a population. How many different coloured dogs or cats or rabbits or chickens or pigeons are there? Or humans for that matter?

Lets say that a pack of wild dogs are dislodged from their planes territory and into a more wooded area. This new circumstance could make their existing camouflage somewhat less effective, and so selection would favour new camouflage patterns or colours. This selection would initially occur from that existing variation, and in subsequent generations this would tend to be further refined with the new mutations each generation inevitably produces. Over the long time scales at which evolution operates this produces camouflage adapted to the local environment.

These same principles apply to pretty much every aspect of the organism in question; limb length, size of teeth, litter size, method of spore dispersal, leaf size and composition, amount of water required......

Yes, it is possible. There are well established models for distribution of mutations, which include population size. For example, taking known human genetic diversity (ie what is visible now in human populations) it is possible to turn the clock back and estimate the number of individuals required in an initial population that would result in the current state of affairs. This has to do with the distribution of mutations in the various ethnic groups around the world, specifically mitochondrial DNA. But also a general principle is at work: in order for a population of animals to be considered stable long term, there is a minimum size of that population, the exact value of which varies from animal to animal and with different contexts. If population numbers drift too low, diversity is also depleted and this is Bad News for long term survival. Thus, because we have thus far survived and even even prospered, we can assume that we didn't drop below that critical threshold. A few thousand individuals is the estimate that the methods have come up with, and they are considered reliable, but still estimates with fairly large error bars.

I'm afraid there isn't one answer to that. Mutagenesis  is by nature a random process, so the exact outcome simply cannot be predicted. This is of course further complicated where there are two nuclei, so some mutations could happen in one and be rescued by the other.

RBC lysis is usually done by sudden changes in osmotic balance. The method I have done uses a binary salt solution, one low, one high. The cells are suspended in the low (hypotonic) salt solution first, which forces water into the cells by osmosis, making them burst. I'm not exactly sure why other cells are not as susceptable to lysis by this method, but I think it must be that they are simply more resistant to osmotic shock. After 30 seconds the high salt (hypertonic) solution is added, bringing the salt level in the buffer to isotonic levels (roughly 150 mM) and preventing further lysis. TE is a very low (hypotonic) salt solution, so I suspect it would quickly lyse RBC in sufficient volumes, though I have never tried it.

The most straight forward way of getting involved is to volunteer. Scientists are notoriously cash-strapped, so are often looking for volunteers to help with their field work. This can, if you are lucky, lead to employment not as a scientist but as a field work labourer or organiser. However, if you are looking to have a career as an academic, you will need at minimum a post graduate degree from a reputable university. I'm sure there are exams to grant a-level equivalence, which would qualify you for the further study you will need to become a working scientist.

Science is a training-heavy career, and there isn't really a way around that.

(posted in Human Biology and Evolution)

I'm pretty sure that we manufacture our own nucleotides, including the nucleobases, mainly out of amino acids. Anyway, all living things contain all four nucleo bases, so you don't have to worry about a special diet.

Very low. Bread is a poor substrate for pathogenic bacteria. The kind which make you sick are almost always found growing on meat or other animal products. You are, after all, made of meat! The most harmful thing you might find is some fungus, some of which can be a little toxic, but they probably won't cause an infection.

Basically, the colder it gets, the slower things grow, so the colder the better. Typically, fridges tun between 2-7 degrees C, freezers at around -15 degrees C. A good rule of thumb is that once it gets cold enough for the water to be frozen, you can be confident that there is little to zero growth going on.

Toasting can certainly kill bacteria. Heating is a highly effective sterilisation method.

(posted in Mammals)

Populations of animals are always evolving. It is a slow continuous process, not a sudden change like a pokemon leveling up.

This kind of extrapolation is very difficult. To predict what might happen, you would have to imagine all of the pressure the cats would be under. This can't be done with any degree of certainty, so we can't predict how cats may continue to evolve in the future.

I agree. Probably not frogs either, I believe frog eggs need to be in water for the tadpole to survive.

(posted in Research and Careers)

Of course not, you have plenty of time!

All laboratory strain of E. coli have specifc genotypes that allow them to be used in specific ways. For example, a common strain is XL1 Blue, which, among other things, has an F' episome under tetracyclin selection. It is also deficient in a DNA methylation enzyme (dam), making it good for plasmid preparations. BL21, a protein expression strain, is often modified with a DE3 phage fragement which expresses T7 polymerase. There are also auxotrophic strains which only grow in the presence of specific chemicals.

To tell the difference between strains, you need to find out their genotype. Unfortunately OP50 is poorly characterised, there doesn't seem to be much about it except that it is a Uracil auxotroph, is streptomycin resistant and useful for growing as food for C. elegans.

http://openwetware.org/wiki/E._coli_genotypes

Hello Matt,

1. "Intelligence" is recently describe to be an emergent property of a large organ, the brain. Generally speaking, greater intelligence requires a higher proportion of your body to be accounted for by brain tissue. Brains, especially large brains, are very complicated and energetically expensive and we divert a disproportionately large fraction of our total daily calories to just maintaining them. In addition to more food, humans pay for our large brains with a slow birth rate compared to many other mammals and high parental investment; The size of the birth canal places an upper limit on head size, requiring much earlier births and helpless young.

If intelligence can be considered a selectable trait, then, like all other traits, it is not always of benefit in all contexts. Therefore, it only arises and comes to fixation in a population which both has the potential AND the correct context for it to be beneficial. For humans and the niche we occupied at the right moment, this worked quite well; our social groups were able to cope with helpless young, and intelligence also greatly aided survival. We certainly had the potential, as you can surmise by recognising some kind of consciousness in our mammalian cousins. For something like an ant, or a rosebush or a jellyfish, the selection forces and context are quite different and therefore the drive towards something you might call intelligence may be weak, non-existant or even negative.

2. I'm not sure about plants and animals "crossing over", I don't think that happened. Plant cells are differentiated from animals primarily in that their ancestors acquired two intracellular symbiotes (symbiogenesis) which eventually became mitochondria and chloroplasts, whereas animal and fungal cells only acquired mitochondria. How exactly all this happened isn't exactly known, but the idea is that one bug tried to eat another, and they ended up doing better together when the eating failed. I suspect that the various invasions of proto-mitochondria happened millions of times before it stuck, and the same is probably true with chloroplasts. Generally speaking it is thought that since plants are the only clade with chloroplasts, they acquired them after mitochondria, which can be found in all eukaryotic cells. Since the mitochondria in all clades of eukaryotes are fundamentally the same (apart from a few hundred million years of very slow evolution), it is consistent with the evidence if this happened in only one population, which then diversified into animals, plants and all the rest.

3. The X chromosome is not disappearing. You may be confused, because according to some recent reports, the Y (male) chromosome is slowly losing genes and therefore getting smaller. This trend is controversial to say that least, and is only a problem if one assumes that there are no natural forces which will cause this trend to halt. Anyway, this isn't terribly interesting; organisms gain, lose and move genetic material around all the time. That it is happening to us is a reassuring reminder that we continue to evolve:)

We (humans) can and do produce amino acids, though only half of the varieties we need. One example is tryptophan. We can't make it, so is considered an essential nutrient because it must be part of our diet. More specificaly, we can't make the side chain of tryptophan, called an idole group. Basically all amino acid backbones are manufactured from sugar and amino groups, the latter recovered from consumed protein. The rate limiting step is usually the acquisition of nitrogen; a historically limited resource, an entire niche of microorganisms is defined by the ability to convert virtually inert nitrogen gas into biologically available ammonia.

While in principle all of the necessary materials are present in a active human cell to manufacture amino acid backbones, it is the derivation of the side chains that is problematic. So in answer to your question, a human cell cannot make most of it's proteins by simply breaking down parts of itself, it needs more externally sourced nutrients to complete it's complement of available amino acids.

Some complementing of things you can't make, like some vitamins, is done by your gut flora, though I'm not sure of the details in this case.

In an interesting aside, because some microorganisms make the amino acids that we don't, they possess synthesis pathways and enzymes that we don't. In pathogenic organisms these unshared biochemistries are attractive targets for anti-microbial drugs, as they minimise the risk of negative interactions with any human proteins which might be related or perform similar functions.

That is a simple question with a very complicated answer.

To be brief, the answer is "maybe".

The possible evolution of a particular characteristic is always subject to caveats and probabilities, because evolution is itself a stochastic non-directed process. Birds, like mammals and reptiles are tetrapods. All four of our limbs were once fins, then legs, then some became arms and wings, and in some cases these became fins again. Taking the example of the cetaceans, where limbs were once again converted into fins, and also the case of aquatic birds where a similar process has occurred, you can see that changing shape and function of limbs is of course possible.

However, when considering such changes it is important to remember that evolution is contextual, forever building on the innovations that came before it. What this means is that if flightless birds (and these are by no means a unified group) were to have their wings altered over generations, there is no reason that they would resemble the grasping hands and arms that their non-avian dinosaur ancestors possessed. Instead, with different genetics and different environmental pressures, I have no doubt that an adequate but different solution would arise.

At one extreme, the kakapo has a full wing, but it's flight muscles are underdeveloped. Then there is the Kiwi, whose wings are tiny reduced nubs and it's feathers are more like downy fur then a flight surface. Both birds are flightless, but I suspect that given the same selection pressures you would have two very different outcomes.

You said "A pair of manipulative arms, would surely be a much better survival asset, than a pair of almost redundant wings."

Again, that entirely depends on the circumstances, and the cost involved in having four active limbs over two. The cost to grow and maintain large muscles and bones is always a consideration. Small, redundant wings might be less useful in certain ways, but they cost much less energy and can still be useful, such as in mating displays, maintaining balance, or keeping warm.

I'm afraid that evolution doesn't provide the kind of specifics you are asking for. The best we can do is describe possible selection pressures that might lead to this kind of structure, or something different that fulfils the same function.

For example:
We can think of these toothed gears as an evolutionary innovation. Like all such innovations, to persist it must be in some manner beneficial, or at least neutral. If perfect coordination of legs is an advantage, then these structures will secure that advantage very well, regardless of how they occurred in the first place. These animals use their legs to jump, so perfect coordination that ensures good aim is a large advantage.

How did the gears arise in the first place? I doubt anyone has much information on that, but if I were to have a guess, I would say that slight roughening on surfaces which interact could, with the correct selection pressures, be developed over generations from simple rough patches rubbing together to heavily ridged rough patches through to full interlocked gears like in the picture. But that is simply speculation.

It looks like a dragonfly to me, an ancient predatory insect, though I couldn't tell you which species you have there. Dragonflies are very widespread throughout the world, and even if you haven't seen them in Scotland before, it is likely that there some native species. Some of them migrate large distances, thousands of kilometres in one case, so they can be seasonal.

Could be this one?
http://news.bbc.co.uk/2/shared/spl/hi/p … html/5.stm

(posted in Evolution)

I would say that they are already in a "tribal" stage, if by tribal you mean a complex extended family social group cooperating to raise young, defend their territory, collect food and even pass on their "culture". Sounds pretty tribal to me.

(posted in Birds)

My Dad used a water gun to discourage a couple of blackbirds from nesting in a tree near his house. It isn't necessary to actually squirt them, just in their general direction, which they certainly don't like:)

(posted in General Biology)

I suspect that prosthetics will become so advanced that a true flesh-and-blood replacement limb wwould no longer be unecessary.

(posted in Research and Careers)

Hello Benjamin,

I did my PhD at Waikato University, so I know Hamilton well.

What you should do next depends on the kind of biology you want to do. If fieldwork is your thing, then there are always people looking for volunteers to help with research and conservation projects. Hamilton has the Maungatautari reserve close by, so contacting the trust running it might be a good place to start. Otherwise go to Forest and Bird or DOC, or try the Biology Department.

If lab-based work is what you want, you options are more limited. The best option is to try to get a summer studentship in a research lab. These are hotly contested, so you will need good marks.

Another simple thing is to go to the biology departmental seminars. You will get an idea on what science is going on and get to talk to the people doing it. An excellent networking opportunity. Good luck!

John

(posted in Evolution)

The situation you describe, where a population is started by only a few individuals, is possible. The reduction of genetic diversity that comes with this extreme genetic bottleneck is called the founder effect. The number of founding individuals necessary for establishing a stable population is heavily dependant on what the new environment is like, eg is there competition from organisms already there? Competition would in general require more diversity to stay viable, whereas if they find an empty niche with plenty of food a population would not be under so much selective pressure. Is the founding organism well suited to the new environment, or will some significant adaptation need to occur for the population to stabilise? Inevitably some adaptation occurs following migration to a new environment, and the extent of this is limited by the existing diversity. Lower diversity means lower chances of successful adaptation and survival.

On the other hand, I would think that very few of these hypothetical island colonisation occur as single, isolated events. If one imagines that, say, a lizard clinging to some driftwood reaches an island simply by the passage of ocean currents, it is reasonable to suspect that another lizard might do the same on the same currents at another time. So, while you are correct in thinking about a theoretical minimum diversity, establishing a population doesn't require that all of the breeding pairs reach the island all at the same time. Instead, successive introductions over a period of years works to keep the gene pool diverse.

It is very difficult to tell, but it looks like a bee or wasp. Carpenter bees have really powerful jaws for boring into wood, and wasps are often predatory with jaws to match. I'm just guessing here, a much better photo is necessary.