Is this not obvious ?

[William Gaatjes]

Biologists attribute variations among individual organisms to differences in genes or environment, or both. But a new study of nematode worms with identical genes, raised in identical environments, has revealed another factor: chance.

I just read this and i feel amazed.
I know the chance factor is a little difficult to prove as a statistic but is this not kind of obvious ? I mean everything inside us and around us just moves about with out guidance. Chemicals are released and because of the infrastructure it will get there sooner or later. In the case of a body that would be the blood stream for example . Inside a cell it would be inter cellar fluid. And this is only when there is no outside influence. While we are non stop invested with all kind of outside organisms. We are at a war which ends when we die. Because then other organisms can take over withOUT being attacked by the defenses of our body. And then there is the non stop ionization and radiation around us. We live in a reactive world. It has to be or their would be no life. It's just another part of epigenetics.

It's another source of variation for scientists to consider. "Researchers have been exploring whether organisms evolve different ways to cope with genetic and environmental variation," said author Scott Rifkin, an assistant professor of biology at UC San Diego. "This study adds random variation to that mix."

Rifkin, who joined the UCSD faculty this fall, completed the study while working at MIT. The paper, co-authored by Arjun Raj, who contributed equally to the work, Erik Andersen and Alexander van Oudenaarden of MIT, is published in the February 18 issue of Nature.

Rifkin and his colleagues looked at the development of the gut in C. elegans. In many, but not all worms with mutations in a gene called skn-1, the gut failed to develop, even when the embryos were genetically identical and incubated together.

"Often when people look at variation in a trait among organisms they try to trace it back to genetic differences or differences in environmental conditions or some combination of the two. In our study there were no such differences, and so we hypothesized that the only other source for the variation could be differences that arose at random during the process of development," Rifkin said.

The mutated gene is the first in a series of several genes that control each other in sequence to determine whether the gut precursors begin to develop into intestinal cells.

In mutant worms, the final gene was either on or off, and that determined whether an embryo developed gut cells or not. But the activity of an intermediate gene varied widely. That's where chance seems to play a role.

Some mutant cells transcribed the gene many times, ultimately creating enough of the protein to activate the final gene. Others made too few transcripts and the final gene stayed off.

DNA winds tightly around proteins, like thread around a spool, and must uncoil for the transcriptional machinery to access a gene.

Some proteins unwind the DNA; others wind it up again. In the mutant worms, the balance shifted to favor the proteins that keep DNA wound. But in some of the worms, the DNA stayed uncoiled long enough to generate sufficient numbers of transcripts to activate the final gene. And so, by chance, those worms developed a gut.

http://www.physorg.com/news185723500.html

 

[DominionSeraph]

I think the method is new. By random mutation alone, I wouldn't expect much variability. This seems to be another avenue by which a gene might express itself.

But I'm also tired, I didn't do an in-depth read, and this isn't an area I've studied extensively.

 

[jackschmittusa]

I can imagine even a random cosmic ray altering a molecule or its connection to another which could lead to a "chance" mutation.

As for a group out of a sample, proximity to a magnetic field, or emf might affect only a portion of the sample closest to the source as the energy drops off so quickly with distance.

 

[William Gaatjes]

double post. sorry.

 

[William Gaatjes]

I can imagine even a random cosmic ray altering a molecule or its connection to another which could lead to a "chance" mutation.

As for a group out of a sample, proximity to a magnetic field, or emf might affect only a portion of the sample closest to the source as the energy drops off so quickly with distance.

I can imagine that too.
Here is my opinion about how evolutionary gaps would happen :

I always wondered if for some reason the following coincidence would arise :

1 More cosmic rays.
2 Higher humidity ( If Henrik Svensmark is right, also an effect of cosmic rays).
3 A weakened field from the sun (but still producing solar winds traveling towards the earth).
4 A weakened magnetic field of the earth.

I wonder if all of this could cause an evolutionary jump. The so called evolutionary gap. The cosmic rays could cause more random mutation under bacteria, viruses, fungi, mycoplasma's, and more complex lifeforms.
Summed up : Viruses, prokaryotes and eukaryotes and the combinations of those ? Because for example our body as is proven is a mix of viruses, bacteria, fungi and ourself. And not just on a seperate level, also on the dna level.

The higher humidity could make it more easy for bacteria and viruses to get from species a to species b. And the weakened fields make it easier for all sorts of high energy particles hitting molecules in our body like proteins, dna, rna and so on.

The cosmic rays and other ionizing radiation would effect all life because this could mean weakened dna repair mechanisms and weakened immune systems.

The chance can arise that a certain complex organism has a weakened immune system, and a weakened dna repair system, gets infected by the not mutated pathogens and gets infected by the mutated pathogens. These pathogens are the bacteria and viruses and fungi and what may exists more. That is a situation what you could call chaos. In effect it is just a extremely large number of random situations that can all come together at 1 point in space and time. The result is a new mutation.

The chance of horizontal gene transfer could increase because of all of this. And all sorts of mutations would arise. What would happen is a wave of mutations followed by a wave of sickness and death followed by species who survived. Different species together living with the "original" species.

This could be the case for land animals and shallow lake and river animals.
But of the deep sea i would not know. It is sad that cosmic rays can penetrate the earth up to the core. That would mean that these cosmic rays can cross the ocean's too. I wonder how the ocean can weaken incoming radiation. Perhaps that is why at the deep sea some animals appear to be frozen in time from a evolutionary standpoint.

Very cold places in the deep sea, hardly have any life. It is the same principle as with humans. If a place arises where there is much food and jobs, a lot of people will go to that place. With animals it is the same they follow the food. Dense packed situations of life increase the chance of mutations as well.

At those thermal vents in the deep, there can be more radiation as well. This would help mutations too. In my phage virus post i added some links about how well adapt some organisms are against radiation. Some bacteria happily thrive next to the uranium rods inside nuclear reactors. Others survive the high energy uv radiation up in the sky.

 

[WinGeek]

I can imagine that too.
Here is my opinion about how evolutionary gaps would happen :

The chance can arise that a certain complex organism has a weakened immune system, and a weakened dna repair system, gets infected by the not mutated pathogens and gets infected by the mutated pathogens. These pathogens are the bacteria and viruses and fungi and what may exists more. That is a situation what you could call chaos. In effect it is just a extremely large number of random situations that can all come together at 1 point in space and time. The result is a new mutation.

This is a very interesting post and worth reading for. Thinking that this could possibly happen in the future, definitely it would be very chaotic. Everyone would like to survive, not just humans but animals as well. Good point of view William.

 

[William Gaatjes]

Thank you.

But i have to point out, that i did not take into account the environment on a chemical level. Maybe certain chemicals also need to rise for such an event.
As an extra effect that has an unhealthy effect on more complex organisms.
So called mutagens come to mind for example carcinogens. These mutagens would have to heave a "natural" origin but can be man made as well.


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

 

[Gibsons]

In genetics, the phenomenon studied here is called incomplete penetrance. Meaning the phenotype associated with the mutation isn't seen in all individuals with the mutation. It's been assumed for while that the reason for this was some stochastic (i.e. random) process, this paper seems to rule out most everything else.

Why the thread jumped from this to disease and immunology, I don't know, but I guess it's to be expected.

 

[William Gaatjes]

In genetics, the phenomenon studied here is called incomplete penetrance. Meaning the phenotype associated with the mutation isn't seen in all individuals with the mutation. It's been assumed for while that the reason for this was some stochastic (i.e. random) process, this paper seems to rule out most everything else.

Why the thread jumped from this to disease and immunology, I don't know, but I guess it's to be expected.

:awe:

 

[jimhsu]

The "humans evolving faster" investigation might be pertinent here: http://www.physorg.com/news116529402.html. One of the best examples is of the LCT gene for lactase becoming essentially fixed in certain populations (European) but virtually absent in others (Asian). The already existing genetic diversity among humans is astounding, to the point that we would probably be seen as separate species by an alien anthropologist.

Realistically, this is why modern genetic experiments are done in massively parallel (i.e. microarrays). The SNR for most useful genetic studies is so low that increasing the sample size is really all that you can do to surpass the stochastic noise.

 

[William Gaatjes]

The "humans evolving faster" investigation might be pertinent here: http://www.physorg.com/news116529402.html. One of the best examples is of the LCT gene for lactase becoming essentially fixed in certain populations (European) but virtually absent in others (Asian). The already existing genetic diversity among humans is astounding, to the point that we would probably be seen as separate species by an alien anthropologist.

Realistically, this is why modern genetic experiments are done in massively parallel (i.e. microarrays). The SNR for most useful genetic studies is so low that increasing the sample size is really all that you can do to surpass the stochastic noise.

I am curious, is there any research done how some humans have aquired the lactose gene modification ?

What i know is little about it, however we all have this gene but with most people this gene is turned of after a few years in child hood. While with others this gene stays active. I assume there are also people where this gene does not function at all. I would like to know how this happened , is there any reasearch done about it ? According to wiki the mutation is located on chromosome 2. By coincidence the gene that made us different from our hairy cousins by fusing chromosome 2 and chromosome 3 from our ancestor ?
(Just some trivial info that popped up .)

I am wondering about the cause ?

I may be interpreting this wrong, but it seems that the tolerance happened after lactose tolerance seem to have started. But that would not make sense, it makes sense that for example it is similair as the theory that the first fish that came on land already had the ability to walk or crawl and had a combination of gills/lungs. The fish did not aquire this after it moved out of the sea on to land. What am i overlooking here ?

 

[Gibsons]

I am curious, is there any research done how some humans have aquired the lactose gene modification ?

What i know is little about it, however we all have this gene but with most people this gene is turned of after a few years in child hood. While with others this gene stays active. I assume there are also people where this gene does not function at all. I would like to know how this happened , is there any reasearch done about it ? According to wiki the mutation is located on chromosome 2. By coincidence the gene that made us different from our hairy cousins by fusing chromosome 2 and chromosome 3 from our ancestor ?
(Just some trivial info that popped up .)

I am wondering about the cause ?

I may be interpreting this wrong, but it seems that the tolerance happened after lactose tolerance seem to have started. But that would not make sense, it makes sense that for example it is similair as the theory that the first fish that came on land already had the ability to walk or crawl and had a combination of gills/lungs. The fish did not aquire this after it moved out of the sea on to land. What am i overlooking here ?

For the fish, think about populations, not individuals. Some survival advantage from flopping onto land, for a brief time - a food source, or escaping predation. If thousands of fish are doing this for thousands of years, eventually some of them will be pretty good at flopping around on land.

For the lactase genes, it seems to be explained by a point mutation in upstream regulatory region. So, just one single base change and the lactase enzyme is produced through adulthood. How it happened originally is impossible to know, it's a simple C/T transition, could've been a million things.

 

[William Gaatjes]

For the fish, think about populations, not individuals. Some survival advantage from flopping onto land, for a brief time - a food source, or escaping predation. If thousands of fish are doing this for thousands of years, eventually some of them will be pretty good at flopping around on land.

Good point indeed, a temporary deficit in water can also be part of the scenario. An extreme example could be a part of a river where the water level almost drops to zero during tides. That could speed up the process indeed.

A few examples.
The names clarify it...

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

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

A possible origin...
http://en.wikipedia.org/wiki/Tiktaalik

For the lactase genes, it seems to be explained by a point mutation in upstream regulatory region. So, just one single base change and the lactase enzyme is produced through adulthood. How it happened originally is impossible to know, it's a simple C/T transition, could've been a million things.

C/T transition : This means charge transfer transition, can you explain more about it ?
First i thought it meant c to t ( Nucleobases like A T G C ). But i assume it means something else.

 

[Gigantopithecus]

I am curious, is there any research done how some humans have aquired the lactose gene modification?

Yeah, that research is pretty extensive at this point. Essentially, the mutations allowing lactase persistence have arisen independently multiple times. Couple times in sub-Saharan Africa, couple times in the Middle East, couple times in Europe.

This is one of the more recent papers and is public access.

What i know is little about it, however we all have this gene but with most people this gene is turned of after a few years in child hood. While with others this gene stays active.

This is exactly correct. LCT is the gene that produces the enzyme lactase; not just all humans but all mammals (unsurprisingly, that's the definition of a mammal, haha) have this gene. So far as has been studied, humans are the only mammals that continue producing lactase into adulthood.

I assume there are also people where this gene does not function at all.

If there are, they would almost certainly die within a few months of birth, unless they were in a modern scientific medicine society. Not being able to produce the enzyme that allows you to digest your only source of food for your first few months = death sentence.

I would like to know how this happened , is there any reasearch done about it ? According to wiki the mutation is located on chromosome 2. By coincidence the gene that made us different from our hairy cousins by fusing chromosome 2 and chromosome 3 from our ancestor ? (Just some trivial info that popped up .)

Haha, interesting idea, but no. There are a lot of genetic changes that have happened that make humans different from our hairy ancestors. (As an aside, we probably haven't been hairy for 2,000,000 or so years.)

I am wondering about the cause ?

I may be interpreting this wrong, but it seems that the tolerance happened after lactose tolerance seem to have started.

This is a good question to have. Here's the deal: the mutation that keeps LCT turned on has happened a number of times in the recent human past. However, before the 'invention' of dairying, what was the point? No one drank milk as an adult before some of us started keeping goats and camels and cows as livestock and started drinking their milk, so there was no selective advantage to those mutations. With no selective advantage, they would have evolved neutrally like any other mutation that doesn't do anything (i.e. neither good nor bad - neutral). Most often, these mutations are eliminated through random chance (genetic drift).

But once you introduce dairying to different societies, the people who can drink milk as adults will be better nourished than those who can't. They will survive longer and have more children, and so on - they will have higher relative reproductive success than other members of the group that can't drink milk as adults. This is why under certain environments, lactase persistence has gone from very rare to very common within a few thousand years.

The environmental parameter in this case is well understood - it's dairying. Other such examples are the evolution of light skin in humans, which has happened (basically) twice - once in Europeans and once in Asians. This is why both Europeans and Asians have light skin but their skintones aren't the same - different mutations of different pigment genes. The ancestral condition for humans is dark skin - but once you leave sunny Africa and head into colder parts of the world, dark skin is not advantageous, it's bad or maladaptive. This is a really neat book written for the interested layperson about skin evolution. The author also talked about her book on the Colbert Report.

But that would not make sense, it makes sense that for example it is similair as the theory that the first fish that came on land already had the ability to walk or crawl and had a combination of gills/lungs. The fish did not aquire this after it moved out of the sea on to land. What am i overlooking here ?

Dunno 'bout that, evolution of lactase persistence makes sense to me...and it's delicious.

 

[William Gaatjes]

The environmental parameter in this case is well understood - it's dairying. Other such examples are the evolution of light skin in humans, which has happened (basically) twice - once in Europeans and once in Asians. This is why both Europeans and Asians have light skin but their skintones aren't the same - different mutations of different pigment genes. The ancestral condition for humans is dark skin - but once you leave sunny Africa and head into colder parts of the world, dark skin is not advantageous, it's bad or maladaptive. This is a really neat book written for the interested layperson about skin evolution. The author also talked about her book on the Colbert Report.

Just a weird question , how does this all relate to vitamin D ?
Vitamin D (which is in reality a sort of hormone that controls calcium uptake and release in the body if i am correct) is also produced in the skin.
I know dairy products are rich in vitamin D.

Here i have an idea :
You could say that in a certain timeframe on earth where there are more clouds and less sun, it also becomes an evolutionary advantage to be able to drink milk. If that lactose gene is still active, it might come in handy to have this gene in long periods of cloudy days. Maybe the food supply has been limited in those specific area's, i mean less sun could mean less crops. Maybe not close to water in the sense that it contains edible fish. A vitamin d shortage can be seriously bad for the health. Thus being able to still process milk which contains lactose could at such a situation be an advantage.
And thus could be a reason to be passed on. It seems that especially pregnant women need a good supply of vitamin D. It is fun to think of a possbile scenario...

 

[KIAman]

Just a weird question , how does this all relate to vitamin D ?
Vitamin D (which is in reality a sort of hormone that controls calcium uptake and release in the body if i am correct) is also produced in the skin.
I know dairy products are rich in vitamin D.

Here i have an idea :
You could say that in a certain timeframe on earth where there are more clouds and less sun, it also becomes an evolutionary advantage to be able to drink milk. If that lactose gene is still active, it might come in handy to have this gene in long periods of cloudy days. Maybe the food supply has been limited in those specific area's, i mean less sun could mean less crops. Maybe not close to water in the sense that it contains edible fish. A vitamin d shortage can be seriously bad for the health. Thus being able to still process milk which contains lactose could at such a situation be an advantage.
And thus could be a reason to be passed on. It seems that especially pregnant women need a good supply of vitamin D. It is fun to think of a possbile scenario...

Modern milk is fortified with Vitamin D. Non-fortified milk is a decent source but not enough to meet nutritional criteria. The Vitamin D used to fortify milk comes from animal skins. So, if cloudy enough to block the Sun's UV all the time, one must sit in front of a UV lamp several times a day because animals will produce less Vitamin D as well, thus no fortification of milk.

Other sources of Vitamin D? Skins. Some plants produce Vitamin D2 but that is inadequate for a single source. Besides, plants need sunlight.

So... basically, if the Earth was cloudy enough to block all incoming UV, we'd be f*cked.

 

[William Gaatjes]

Modern milk is fortified with Vitamin D. Non-fortified milk is a decent source but not enough to meet nutritional criteria. The Vitamin D used to fortify milk comes from animal skins. So, if cloudy enough to block the Sun's UV all the time, one must sit in front of a UV lamp several times a day because animals will produce less Vitamin D as well, thus no fortification of milk.

Other sources of Vitamin D? Skins. Some plants produce Vitamin D2 but that is inadequate for a single source. Besides, plants need sunlight.

So... basically, if the Earth was cloudy enough to block all incoming UV, we'd be f*cked.

Well, there is still an advantage when drinking milk. If you add eggs to the picture even more. When drinking the milk you do not have to kill the animal.

Eggs can be a possibility, some farmers who have cows or goats could also have had chickens.

The idea a bit extended :

No Fish rich diet.
Less Sun.
Eggs.
Milk.

Then you do not have to skin your stock and still have a net amount of vitamin d then without drinking milk. Although i do not know if living on eggs alone is sufficient to keep the amount of minimal vitamin d above a minimum required level. And afcourse, when you have a population, means you have to share the resources in this case the food. I guess it all comes down to the amount of food and necessary nutrients present. The scenario could be that the strongest and most aggressive person eat the most , but i do like to think that one of the advantages of humans is that humans are a lot more social then that.

EDIT :

But in any way, it was just an idea. It is not a hypothesis i am proposing.

 

[Gibsons]

C/T transition : This means charge transfer transition, can you explain more about it ?
First i thought it meant c to t ( Nucleobases like A T G C ). But i assume it means something else.

It just means changing a C to a T, that's all. Well, the corresponding base changes from G to A, but that's sort of assumed.