Darwin re-visited

[maikeru]

Wow!

So many heavy posts

So little time

Just a comment on the above.

Chewing cocaine leaves helps O2 'whatever' assimilation? at high altitudes. So did the plant evolve to help the Indians do you think? It has certainly ensured its (the plant's) survival ?:eek: :doh:

I will have a BIG THINK about other posts and come back

 

Sorry about the heavy posts. :) I think it does, because cocaine stimulates the central nervous system, and makes the heart beat much faster, raises blood pressure, and probably through those means helps to disseminate O2 through the body.

 

Cocaine is an alkaloid, part of a chemical family which probably evolved to kill insects or discourage animals--i.e., toxins. LSD is also a famous alkaloid, though derived from rye ergot fungus, IIRC.

 

That humans can benefit from chewing coca leaves in this case is a side effect of cocaine's general purpose, which is probably to cause the nervous system of an insect to go bonkers and kill it. Humans are a lot bigger obviously, probably have different ways to detoxify it than insects do, and don't suffer as much. Same thing with caffeine and theobromine, which also kill insects that feed on the plants that have them. Except that humans can detoxify those quickly and without problem, so that they actually seem to have some beneficial effects for us.

 

PS

Could you please paragraph or even break after sentences with posts? Otherwise it is like being hit over the head with a typewriter.

 

I'll try. I know it's tough enough for people to get the obscure details of what I'm talking about, and having big paragraphs just makes it worse. I have inherited some bad habits from reading a lot of science papers and textbooks. :(

 

PSS

How come i get this:-

"You must spread some Reputation around before giving it to maikeru again.";

when you are not showing any rep power?

 

I am not sure... I have no rep though.

[erKa]

.... There are some gene "superfamilies," such as the Immunoglobulin, or Ig, superfamily (one which plays a role in so many proteins of the immune system), in which hundreds of genes are all related to some primordial gene, and if extended, could include dversions or different genes that are related, but silent or nonfunctional, because of mutational or expressional problems (such as a gene could still be transcribed, but one of the regulatory processes used in gene transcription or translation, which leads to a gene ultimately being expressed, might destroy its expression--and thus no gene expression/protein)....

 

This part of the theory is the most cryptic: if natural selection causes by mutation a new gene after the stroke due to external environment in a taxon why the same gene had to be hidden in the inactive DNA instead of forgetting it at the end of external interference? Why some genes look to accomplish this strange rule and others not at all? Who superseeds the rule? There must be an extra unknown rule.

[HydrogenBond]

If one looks at a virus inserted into the DNA, the question becomes how does it know how to do this and where to go? It is not a viable lifeform nor does it have any intelligence yet it knows where to go. The reason has to do with equilibrium hydrogen bonding. When it enters the cell, it flows down the hydrogen proton gradient to an equilibrium position on the DNA.

[CraigD]

If one looks at a virus inserted into the DNA, the question becomes how does it know how to do this and where to go? It is not a viable lifeform nor does it have any intelligence yet it knows where to go. The reason has to do with equilibrium hydrogen bonding. When it enters the cell, it flows down the hydrogen proton gradient to an equilibrium position on the DNA.

This is not what molecular biologists whom I have read or spoken with on this subject believe. :wave: Research indicates that viruses contain surface proteins that “recruit” specific topoisomerases, enzymes necessary for normal cellular protein expression.

 

Viruses therefore insert their DNA at the same sites cut by specific topoisimerases. A virus can be said to “know” where it will go, in a very vague and limited sense, by these specialized surface proteins.

 

Some of the most effective antiviral therapies involve drugs that selectively bond with specific topoisemerases, inhibiting their bonding with viral surface proteins.

 

Despite their small size and limited capabilities, viruses are physically complex and highly evolved organisms!

[HydrogenBond]

This is not what molecular biologists whom I have read or spoken with on this subject believe. Research indicates that viruses contain surface proteins that “recruit” specific topoisomerases, enzymes necessary for normal cellular protein expression.

 

But even those combine via hydrogen bonding with the attraction also due to equilibrium hydrogen bonding. In other words, they avoid other potential hydrogen bonding throughtout the cell until they find the correct hydrogen bonds for stable equilibrium. This alters the local equilibirum triggering other hydrogen bonding events.

 

Here is an interesting thought that came to me this morning. If one looks at a virus and sperm cell they sort of have that cellular penentration, migration and alteration of the DNA in common. Maybe virus were the precursors to sperm cells before true male-female differentiation was common place. Just some food for thought.

[CraigD]

This is not what molecular biologists whom I have read or spoken with on this subject believe. Research indicates that viruses contain surface proteins that “recruit” specific topoisomerases, enzymes necessary for normal cellular protein expression.

But even those combine via hydrogen bonding with the attraction also due to equilibrium hydrogen bonding. In other words, they avoid other potential hydrogen bonding throughtout the cell until they find the correct hydrogen bonds for stable equilibrium. This alters the local equilibirum triggering other hydrogen bonding events.

I don’t mean to give the impression that H-bonding isn’t very important to the dynamics of molecular biology, or that HBond, who I recall is a professional chemist, doesn’t have expert understanding of and interesting insights into this chemistry.

 

I got the metaphorical impression from post #71 of a virus finding an insertion site on nuclear DNA like a rolling ball finding a low spot on an uneven parking lot. The actual dynamic, as best I understand it, is more like a burglar sneaking into you yard, stealing your guard dogs from their kennels, and then wandering around your house until they find an screen door they can chew through.

Here is an interesting thought that came to me this morning. If one looks at a virus and sperm cell they sort of have that cellular penentration, migration and alteration of the DNA in common. Maybe virus were the precursors to sperm cells before true male-female differentiation was common place. Just some food for thought.

That is an interesting thought.

 

I don’t think it’s what happened.

 

In response to Edge’s 2005 world question, "What Do You Believe Is True Even Though You Cannot Prove It?", Lynn Margulis expressed the opinion that all complex multicellular animals evolved from colonies of a single kind of single cell-organism with the head/tail structure common to both sperm cells and modern spirochete bacteria. I find her reasoning compelling. If correct, the modern form of sperm cells did not evolve from a simpler cell or organism such as a virus, but is the same as that of the earliest cells in the evolution of sperm-producing animals.

 

The idea that single cell organism like bacteria evolved from organisms like viruses, however, is attractive, and could be true.

[hallenrm]

Thanks Craig for providing an excellent link. A very interesting feast of thoughts ! :evil:

[kaminarigaston]

I'd like to dispell some misconceptions, that evolution has a goal and that evolving is improving.

 

 

Most (all?) languages are based on this:

 

someone (the subject) performs an action (the predicate)

 

But, really, when IT SNOWS, could you please tell me who is IT that is SNOWING.

The entity EVOLUTION doesn't exist, OK? It's just a name that we give to a bunch of complex interactions. And as it is not an entity, it DOESN'T WANT ANYTHING. You can say the same about life, nature and any non-personal mental construction.

Evolution doesn't have a goal, and life doesn't seek to survive. Teleology has no place here.

When you say that an organism adapted to an environment, you are saying that it is more likely for that organism to survive in that environment. But, you know, sh*t happens and maybe sh*t will happen to it. That's the thing about probability, it's just, you know, PROBABLE. And EVOLUTION won't care about it cause EVOLUTION is not an entity with a goal, OK? But organism better adapted to an environment will statistically survive over less adapted organisms. Probably. In the long run. Or not.

That is evolution, OK? Nothing more than a gamble, ruled by chance and represented by statistics.

 

And when we talk about the survival of the fittest (wich is only the most PROBABLE outcome), we should always keep in mind that fitness is RELATIVE. There are no umbrella solutions in life, you always get adapted to a CERTAIN environment, OK? We humans may forget it cause our spiffy intellect has proved to be quite the Swiss knife. But don't forget that an individual of our advanced life form would die in the most primitive trylobite's environment. What would bees sofisticated adaptations would amount to if there were no flowers? And guess what, when you adapt to an environment you change it cause you are really a part of it. So the rules to fitness are always changing! Evolution is just change, not improvement, and if I may say again, it doesn't have a goal.

That's why it could become in special circunstances, like a rock, scissors and paper game. An environment gets rocky, so the organism gets papery, but that turns the environment scissory, wich makes the organism rocky... Oh, you get the picture.

[Michaelangelica]

I'd like to dispell some misconceptions, that evolution has a goal and that evolving is improving.

it is a common miss-conception probably from economists using the words "Survival of the Fittest"

It is important that we all understand biology because of the incredible influence it has on our cultural ideas and values.

Look at the current bizarre debate on stem cells.

Human eggs without a receptive uterus are about as useful as supermarket chicken eggs.

 

it DOESN'T WANT ANYTHING. You can say the same about life, nature and any non-personal mental construction.Evolution doesn't have a goal, and life doesn't seek to survive.

 

I don't know if i entirely agree. It wants to survive; surely this is the point?

 

Life may or may not have other conscious, directed purposes. I don't think we know enough yet to put that idea to bed.

That 97% of Junk DNA worries me. What if it is left over bits of code from the 99.99% of life that has gone extict, so far, on Earth?

 

That's why it could become in special circumstances, like a rock, scissors and paper game. An environment gets rocky, so the organism gets papery, but that turns the environment scissory, wich makes the organism rocky... Oh, you get the picture.

The environment both in-utero and out-utero changes the stuff of life.

 

hydrogenbond

Here is an interesting thought that came to me this morning. If one looks at a virus and sperm cell they sort of have that cellular penentration, migration and alteration of the DNA in common. Maybe virus were the precursors to sperm cells before true male-female differentiation was common place. Just some food for thought.

Interesting thought. Has anyone looked at this? Nature seems to conserve a lot of its cleverist inventions.(ie the eye) You may be right.

You need some quantum biology to prove it?

 

Thanks Craig.

Marguis is a facinating biologist. Any suggested reading?

[Michaelangelica]

How fast is evolution?

This was an interesting TV show tonight.

.

These DNA timescales worry me. How can we know the rate of evolution when some organisms don't evolve at all?

 

There are human traits that have appeared in the last 10,000 years ( eg lactose tolerance, Tibetan breathing at high altitudes, "Chinese" reaction to alcohol, African malaria resistance, plague induced Aids resistance). There may be lots more.

 

Natural selection tell us that change is slow and random. I am not comfortable with that.

 

Here are bits of the transcript of the show and the web-link.

 

Dr Chris Burridge: We're thinking about how long ago things happened in the past and also the rate of DNA change which underlies all evolution.

 

Since the late 70's, we've assumed that our DNA changes, or mutates, at a rate of around 1 to 2 per cent every million years.

 

Jon and Dave set out to calibrate the molecular clock. This led them to the valleys and rivers of the Marlborough Sounds.

 

Associate Professor Dave Craw: This is where the geological things are happening quite fast, very quickly in relation to other parts of the world.

 

Narration: This kind of event is very useful because when a river splits in two its fish population is also divided in two.

so there's been DNA substitution going on there over the last one hundred thousand years.

 

Narration: These fish were separated for a relatively short time in evolutionary terms, but were showing relatively huge differences in their building blocks.

 

Dr Jon Waters: We were really, really surprised by this. The amount of genetic change we're looking at here is an awful lot more than we would have predicted.

 

Narration: Rather than mutate at a rate of around 1 to 2% every million years, Dave, Chris and Jon's discovery suggests DNA is mutating up to 10 times faster.

http://www.abc.net.au/catalyst/stories/s1778907.htm

--

[Michaelangelica]

"When we're frightened the hair on our skins stands up, just like it did when we had fur.

We are history!

Everything we've ever been on the way to becoming us, we still are. . . . .

. . .

'I'm made up of the memories of my parents and grandparents, all my ancestors.

They're in the way I look, in the colour of my hair.

And I'm made up of everyone I've ever met who's changed the way I think.

 

So who is "me"?'

 

Page 304, A Hatful of Sky, Terry Pratchett

[Michaelangelica]

Just interesting

That's all

http://www.firstscience.com/site/editor/0161_ramblings_30102006.asp

A medical student she knew was examining cadavers as part of her anatomy course when she came across a body that looked relatively normal - but had a slight oddity about it that she couldn't quite figure out.

She called her lecturer over to have a look, and after a moment of confusion, he realized what the peculiarity was: the person's internal organs were flipped left to right!

 

In most of our bodies, the heart, stomach, pancreas and spleen are found on the left-hand side while the liver and gall bladder are on the right. But for about 1 out of 10,000 people, the internal organs are flipped laterally and so are found on the opposite side than one would expect.

In most cases, this doesn't cause any problems whatsoever, in fact some people - like the one the medical student was examining - can live their whole life without even knowing that their organs are reversed.

 

The condition is known medically as situs inversus and was first identified in 1643 by Marco Severino, an Italian surgeon.

More than a century later, it was studied further by Scottish physician Matthew Baillie. It is a recessive genetic condition - meaning that a person must have two copies of the gene for it to be expressed.

Some people are carriers of the gene (i.e. have only one copy of the gene and so have normal organ symmetry) but if they were to reproduce with another carrier, could pass on the condition to their offspring if they were to inherit both recessive genes.

 

But how exactly does this condition occur? How do our organs happen to be placed on the left or right and why is this different for some people?

[HydrogenBond]

Narration: Rather than mutate at a rate of around 1 to 2% every million years, Dave, Chris and Jon's discovery suggests DNA is mutating up to 10 times faster.

 

What this shows is how important environmental changes are to rate of evolution. The data shows how natural progressions of the earth causes genetic changes to accelerate. One only has to considers how quickly humans has evolved over the past 10,000 years, due to man-made or rapidly changing cultural environments. The DNA plays a support role which acts as a capacitance that records the change. Small or slow local environmental changes create small genetic changes while large or faster environmental changes create large and faster genetic changes.

 

An interesting correlation is the rate of evolution as a function of geological changes. In other words, the earth itself is helping to evolve life by its own geological evolution.

 

The problem with this premise is connected to the philosophical bias within the life sciences. It assumes genetics works independantly to create random pertubations with selective advantage. If the environment changes, those with selective advantage stand out and begin to dominate. The reason for this bias is that there is not a good mechanism by which environmental changes feedback to the DNA directly.

 

But there is such a mechanism. It is connected to hydrogen bonding. Cells are composed primarily of water and are bathed in more water. The basis for the properties of water is hydrogen bonding. Liquid water is in a state of dynamics hydrogen bonding. The DNA is also based on hydrogen bonding and itself is bathed in water. There is a connection between the external and internal water and the internal water and the DNA via the hydrogen bonding.

 

It is not cooincidental that the most abundant material in the universe, i.e, hydrogen, plays a pivot role in nature's highest expression, i.e, life. If we take away the dynamic and static hydrogen bonding from life, life returns to a sludge. Yet this dynamic glue is not considered important. Where is the logic there. It sounds like beaurocratic thinking, which does not allow one to think for themselves.

 

This the second problem with the life sciences. It is based too much on experiemental empiricism. Such science does not really require logic but only following the procedures of beaurocratic science. Without the requirement or the practice of logic, even simple logical connections seem to fly over everyone's head.

[Michaelangelica]

has anyone seen this?

Human Genographic Project

Science Show - 2 December 2006  - Genographic project and everyday reductions in carbon emissions

Since we started the project, just over a year and a half ago now, we've sold 170,000 of the cheek swab kits, which is extraordinary. They're $US100 each, you can buy them at nationalgeographic.com, and it will tell you which haplogroup you belong to. So it will tell you about your deep ancestry going back up to 60,000 years...

 

Robyn Williams: Looking at your DNA.

 

Kim McKay: ...looking at your DNA. I did it and I found out (surprise, surprise) I'm part of haplogroup H

[Eclogite]

One only has to considers how quickly humans has evolved over the past 10,000 years, due to man-made or rapidly changing cultural environments.

This startled me. What is the nature of this evolution? What is the evidence for it? I see an enormous change in man's character unrelated to genetics, but to culture and civilisation. The genotype, surely, is relatively unaltered.

[skuzie]

The genotype, surely, is relatively unaltered.

 

The genotype changes as time goes by and it changes faster as a species is stressed or its lifestyle dramatically changes. I would say our lifestyle has changed for the last 10,000 years. Say certain genes become more popular and certain genes are less popular because of the current mating selections, the popular ones will surge and overtake the whole species and the not popular ones will wash down and dissapear. I wonder how condoms and birth control will change us for the next couple hundren years, i have a feeling its going to be very dramatic.

 

"The evolution of human beings has consisted largely of adaptation to one another" - Robert Wright in 'The Moral Animal'

[Rade]

...The genotype, surely, is relatively unaltered.

Perhaps not--see article below from New Scientist, 2006:

 

Human genes involved in metabolism, skin pigmentation, brain function and reproduction have evolved in response to recent environmental changes, according to a new study of natural selection in the human genome.

 

Researchers at the University of Chicago, US, developed a statistical test to find genomic regions that evolution has favoured over the last 15,000 years or so – when modern humans dealt with the end of the last ice age, the beginning of agriculture, and increased population densities.

 

Many of the 700 genes the researchers identified – especially those involved in smelling, fertility, and reproduction – are also suspected of having undergone natural selection during the divergence of humans and chimpanzees millions of years ago.

 

But some of the newly identified genes fall into categories not previously known to be targets of selection in the human lineage, such as those involved in metabolism of carbohydrates and fatty acids.

 

“It’s reasonable to suspect that a lot of these are adaptations in response to new diets and agriculture,” says team member Jonathan Pritchard.

 

For example, gene variants that improve the digestion of lactose have become more common, presumably since the domestication of cattle provided a ready source of milk. And in some Europeans, genes giving a lighter skin have increased in frequency, as populations have moved north to regions where there is less sunlight to generate vitamin D.

 

The researchers analysed the genomes of 209 people from Nigeria, East Asia, and Europe. They found widespread signals of recent selection in all three populations.

 

Only one-fifth of the 700 genetic regions identified were shared between at least two of the groups – the rest were unique to single populations. That supports the idea that the adaptations are recent, Pritchard explains.

 

The statistical test is a “powerful way of looking for selection in the genome”, says Michael Hammer of the University of Arizona in Tuscon, US. It looks for certain patterns of DNA – called linkage disequilibrium – that show a gene variant is young. It then identifies those that appear at high frequencies, which suggest they have been selected for.

 

Definitive proof that the gene variants are being favoured in the human genome will require detailed analysis of the changes they cause in proteins and how this affects fitness. But Hammer says “they’ve given us a huge list of candidates".

 

Nonetheless, there are likely to be many more, says Peter Andolfatto of the University of California, San Diego, US: “The genes being mapped here at best probably account for only a small fraction of the targets of recent selection in the human genome.”

 

Identifying the gene variants that are under selection may one day help medicine, Pritchard adds. That is because individuals with a newly evolved gene variant may be better adapted for modern human conditions and less susceptible to certain diseases. Understanding the differences could help guide future therapies.