Denial of evolution IV

[Hercules Rockefeller]

As per the first three Denial of Evolution threads (here, here and here), this fourth instalment is also a quarantine area for threads that blindly regurgipost all the usual creationist/evolution denialism stuff, such as:

-- scientists know that evolution is wrong, but are hiding that fact in order to retain their power;
-- evolution is just a theory;
-- Darwin recanted on his deathbed;
-- no one has seen a bacterium evolve into a fish;
-- there are no transitional fossils;
-- speciation has never been seen;
-- okay, speciation has been seen, but the creation of new Genuses has not;

....and everything else which is summarily smacked down by everyone who passed high school biology.

 

[Zenithar66]

The nitrogen problem?(evolution of life)

This is my first post on this thread. I have been deeply studying evolution and other subjects and now feel i am in a position to debate my points and learn from others. My posts will be mostly about evolution/biology.

ANYWHO...

today i was doing a bit of reading on a creationist blog(I am not a creationist and hold know theistic leanings).
But he brought up a very strange and seemingly pertinent point that i have since researched..

The jist of his argument was that cyanobacteria(and some others) are required for life to exist, the reason being that nitrogen(comprising some 78% of our atmosphere) is totally useless to plants in its normal state.
It must be converted by these cyanobacteria into usable compounds which the plants can then utilize for vital life processes.(Amazing in and of itself, )..

Now, DNA as well as RNA and amino acids, as we all know, are kind of important when it comes to....being alive! DNA adn amino acids incorporate nitrogen into its bases and the central molecule of amino acids is nitrogen.

it seems there may be a loop or snag if we try to look back(kind of chicken and egg i suppose)..

so since cyanobacteria fix nitrogen, and cyanobacteria have DNA.

how could life "get started" since any DNA need nitrogen in its amino acids and bases, yet, they cannot use nitrogen unless cyanobacteria(which wouldnt exist without the dna) performs its alchemy on it?

Is this a problem to an inorganic beginnig to life, or a problem in any way?

This is more of a general specualtion but my later posts will be on much more detail..

 

[Walter L. Wagner]

Lightning fixes nitrogen. Read up on the Miller-Urey experiments for making life precursors. http://en.wikipedia.org/wiki/Miller–Urey_experiment

And welcome to SciForums.

 

[iceaura]

today i was doing a bit of reading on a creationist blog(I am not a creationist and hold know theistic leanings).
But he brought up a very strange and seemingly pertinent point that i have since researched..

You haven't researched it, obviously.

In the first place, there are several chemical pathways that can fix nitrogen from the primordial atmosphere into many and diverse chemical compounds without involving living beings - lightning powers a couple of them, and you would have found several others with even rudimentary efforts.

In the second, there is no requirement that the early complex arrangements from which modern life emerged necessarily involved much nitrogen at all - evolutionary theory specifically and fundamentally allows precursors to differ from further evolved arrangements in almost any way.

There is no point in spending time reading "creationist blogs", unless you are doing sociological research into US political factions. If you do plan to waste further time thusly, you needn't inform this forum of your findings - they are not breaking news, around here.

 

[Zenithar66]

okay, so basically your saying it "could" have been lighting, to me this is not definitive, i read that lighting only contributes a minute amount to fixed nitrogen.

Oh, and alhough many creationists are..we IDiots, i would never decline from reading there blogs as they present fascinating information about nature!

thanks for the warm welcome!

 

[iceaura]

okay, so basically your saying it "could" have been lighting, to me this is not definitive

As was pointed out to you:

You haven't researched it, obviously.

Oh, and alhough many creationists are..we IDiots, i would never decline from reading there blogs as they present fascinating information about nature!

How can you tell? Without other sources, you never know whether they are even - they are, sometimes - simply lying to you. This silliness about nitrogen should warn you off - you are not able to weed out the bs, and therefore you cannot acquire "information" about nature from a creationist blog.

Many other sources present fascinating information about nature. Read them instead.

 

[Fraggle Rocker]

i read that lighting only contributes a minute amount to fixed nitrogen.

Well of course that's true, today. There are so many other, more powerful nitrogen-fixing processes in place that lightning is just a statistical footnote. But four billion years ago those other processes didn't exist yet, and there was considerably less nitrogen being fixed. On that much smaller scale, lightning was a major contributor.

Oh, and although many creationists are..well idiots, i would never decline from reading there blogs as they present fascinating information about nature!

I would not recommend trusting anything you find on a creationist website to be actual "information." They have taken intellectual dishonesty to a new plateau.

As many of the members know and will therefore stop reading at this point, my wife and I went to a debate between a "creation scientist" and a real scientist, sponsored by CSICOP, 25-30 years ago when the Religious Redneck Retard Revival had become a major force in American politics and culture.

The creationist was very articulate, a much better speaker than the academic, and he was clearly well educated. He had carefully reviewed the fossil record and pulled out a non-random sample of specimens which, by themselves, appeared to illustrate his point. For supporting documentation, he referred to poorly (if at all) peer-reviewed papers from third-rate universities funded by Christian fundamentalist sects, such as Pasadena's Ambassador College.

He obviously knew that he was lying. And he was an "authority" that the creationist movement selected as their spokesman.

thanks for the warm welcome!

You have to have a thick skin to get along here. Looks like you'll do fine.

 

[Trippy]

okay, so basically your saying it "could" have been lighting, to me this is not definitive, i read that lighting only contributes a minute amount to fixed nitrogen.

Oh, and alhough many creationists are..we IDiots, i would never decline from reading there blogs as they present fascinating information about nature!

thanks for the warm welcome!

My recollection is that the diatomic Nitrogen currently found in the atmosphere is (largely) the result of the photochemical breakdown of Ammonia, which was present in the primordial solar nebular, and has been observed in comets.

Additionally, Ammonia (along with amines) has been found in the Murchison Meteorite and the Tagish Lake Meteorite not to mention its presence in Titan's Atmosphere. Because Nitrogen is the 4th most abundant element in the universe, it has been suggested that Ammonia Hydrates may have a role to play in cryotectonicism in the outer solar system.

So the 'issue' is really a non-starter

 

[Zenithar66]

Well of course that's true, today. There are so many other, more powerful nitrogen-fixing processes in place that lightning is just a statistical footnote. But four billion years ago those other processes didn't exist yet, and there was considerably less nitrogen being fixed. On that much smaller scale, lightning was a major contributor.I would not recommend trusting anything you find on a creationist website to be actual "information." They have taken intellectual dishonesty to a new plateau.

As many of the members know and will therefore stop reading at this point, my wife and I went to a debate between a "creation scientist" and a real scientist, sponsored by CSICOP, 25-30 years ago when the Religious Redneck Retard Revival had become a major force in American politics and culture.

The creationist was very articulate, a much better speaker than the academic, and he was clearly well educated. He had carefully reviewed the fossil record and pulled out a non-random sample of specimens which, by themselves, appeared to illustrate his point. For supporting documentation, he referred to poorly (if at all) peer-reviewed papers from third-rate universities funded by Christian fundamentalist sects, such as Pasadena's Ambassador College.

He obviously knew that he was lying. And he was an "authority" that the creationist movement selected as their spokesman.You have to have a thick skin to get along here. Looks like you'll do fine.

well you certainly cant judge a movement by a person, It seems people here are slighly close minded about the issue and just brand all creationists under the same heading?

I am more open and i know there is bs on both sides, dosent stop studying them...
but thanks, it seems the nitrogen issue is not an issue in terms of the current theory, but of course I have many more questions and hope for replys!!

 

[Zenithar66]

A Very ropey question!(Topoisimerase')) Problem?

Okay, first off I just want to say that, although I am interseted in many feilds of science, evolution, its mechanism and its assumed results has truly fascinated me and I will indeed be posing questions for "evolutionists"(silly word really) to try to answer. (should they feel like it)

This is by no means to try to "get one over" or prove the existence of a god etc, nor do I claim that, if evolution is proved wrong, therefore intelligent desing or any of that. I am simply sick of constany studying and not having anybody rebute me, how can I know if im on the right track if im not activley being rebutted!

at the end of the day, my current position(after reserach, and this position is open to change unlike theists etc) is that evolutions proposed mechanisms are not enough to account for what we actually witenss in nature. And not only that but that faith is a huge part of evolution, or rather its mechanisms what with co evolution of parts etc etc(i will have more on this later)..

but anyway, I truly dont want to come across as picking hoels in it becuase it dosent agree with my world view, but I wont deny i want to pick holes in it and for the simple reason to see does it hold up!

any way i do have a question at the end of all this!

Topoisimerase 1 and 2(as im sure you guys interested in molecular biology know) is a staggeringly beautifull enzyme that performs an even more amazing task.

the problem arises when DNA becomes "supercoiled". If you imagine during the replication process as helicases(I'll come back to them later.....dont hit me!!) are winding and unwinding the dna, tagles will arise ahead of the replication fork!..so there is an elegant and frankly jawdropping solution to this problem.

Topo 1 comes in and cuts a single dna strand to releive the pressure created by the tangle! It litearlly cleaves DNA and actualy passes the strand through another break(topo 2 does this) and therefore erradicating one full loop in the supercoil and letting the replicaton machinery(moving 1000 ntides p/s in bacteria!!) continue its life saving job of creating the new strand...

this

so, if we imagine this enzmye from an evolutionary perspective(I literally found 3 papers online dealing with it, hence i come here...i dont have membershp on any sites to look at papers...damn!) then wouldnt we have to assume that the very first time DNA supercoiled, that topisimerase or an analog that cleaves DNA in just the right palce would have to be present for the continuation of life. And if so, can we prove this or simply guess, and if we guess is it not a leap too far to extrrapolate this situation? Bearing in mind that teh ATP binding sights would have to be already present as well as ATP?

so...and this will be the essense of my questions on these forums..

fact or faith?...too far a leap or sensible extrapolation?

thanks for your time guys!

P.S i will indeed go into more detial on the mechanisms when answering

 

[Zenithar66]

Hmmmm

Mod note: moved from Fish to amphibian transition thread.

well, i feel all the answers in this thread are based on alot of specualtion...
what i dont understand is why you try to figure out why it evolved, rather then how it could have?

a few fossils certainly dont talk to the thousands of molecular and macro changes that would had to occur to take somethign out of the sea!
not to mention lots of this would simply have to co ordinated by a blind process for the organism to survive at all.

and others are right, there is no direction for evolution, just evolution.
Saying that, as others have, it would have been more advantageous means nothign but stating the very obvious, it explains nothing about the origin of the staggering and many adaptions needed.

The issue is far from settle, i.e, can evolutions mechanisms be up to the task you are setting it. As we know, fossils are not definitive proof that this occured, but rather evidence in favour!

 

[yaracuy]

[






Topoisimerase 1 and 2is a staggeringly beautifull enzyme that performs an even more amazing task.

the problem arises when DNA becomes "supercoiled". If you imagine during the replication process as helicases( are winding and unwinding the dna, tagles will arise ahead of the replication fork!..so there is an elegant and

Topo 1 comes in and cuts a single dna strand to releive the pressure created by the tangle! It litearlly cleaves DNA and actualy passes the strand through another break(topo 2 does this) and therefore erradicating one full loop in the supercoil and letting the replicaton machinery(moving 1000 ntides p/s in bacteria!!) continue its life saving job of creating the new strand...

this

so, if we imagine this enzmye from an evolutionary perspective(I literally found 3 papers online dealing with it, then wouldnt we have to assume that the very first time DNA supercoiled, that topisimerase or an analog that cleaves DNA in just the right palce would have to be present for the continuation of life. And if so, can we prove this or simply guess, and if we guess is it not a leap too far to extrrapolate this situation? Bearing in mind that teh ATP binding sights would have to be already present as well as ATP?

so...and this will be the essense of my questions on these forums..

fact or faith?...too far a leap or sensible extrapolation?

thanks for your time guys!

P.S i will indeed go into more detial on the mechanisms when answering[/QUOTE]
mmmmmmmmmmmmmmmmmmmmmmmmmm

Slightly condensed version.

In the process of cutting and splicing does it cut along the gene ?

 

[Zenithar66]

reply

im not quite sure i understand your reply? if your asking does it cleave the genes then no, it simply cleaves the phosphodiester bakcbone of the DNA duplex.

Oh, and then re seals it of course!

 

[Pete]

Topoisimerase 1 and 2(as im sure you guys interested in molecular biology know) is a staggeringly beautifull enzyme that performs an even more amazing task.

the problem arises when DNA becomes "supercoiled". If you imagine during the replication process as helicases(I'll come back to them later.....dont hit me!!) are winding and unwinding the dna, tagles will arise ahead of the replication fork!..so there is an elegant and frankly jawdropping solution to this problem.

Topo 1 comes in and cuts a single dna strand to releive the pressure created by the tangle! It litearlly cleaves DNA and actualy passes the strand through another break(topo 2 does this) and therefore erradicating one full loop in the supercoil and letting the replicaton machinery(moving 1000 ntides p/s in bacteria!!) continue its life saving job of creating the new strand...

this

so, if we imagine this enzmye from an evolutionary perspective(I literally found 3 papers online dealing with it, hence i come here...i dont have membershp on any sites to look at papers...damn!) then wouldnt we have to assume that the very first time DNA supercoiled, that topisimerase or an analog that cleaves DNA in just the right palce would have to be present for the continuation of life. And if so, can we prove this or simply guess, and if we guess is it not a leap too far to extrrapolate this situation? Bearing in mind that teh ATP binding sights would have to be already present as well as ATP?

I found a few articles.
Bear in mind that this is a detective story - you're not likely to find definitive answers to things that happened billions of years ago, only ways that things might have happened that are consistent with what we can observe now. (Many creationists seem to hate that. They seem to hold 'science' to a different standard.)

My understanding of molecular evolution in general is that new functions often evolve from older similar functions.

It seems clear that supercoiled DNA would not be possible without mechanisms to split and join DNA.

If so, then mechanisms to split and join DNA must have existed before supercoiling.

If so, there must a use for those mechanisms before supercoiling - like DNA or RNA repair mechanisms?

But I'm speculating. Here are some recent articles that look interesting and relevant (for the possible evolution pathways of the supercoiling mechanism, the possible selection pressures, and for the detective work involved), but that I haven't read. Let me know which ones you can't access the full text.

2007 - Origin and evolution of DNA topoisomerases.

2009 - Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

2008 - A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya.

2010 - Structure, Function, and Evolution of Linear Replicons in Borrelia (See the section on evolution of telomere resolvases)

2010 - A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs

2009 - DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway

2010 - Evolutionary twist on topoisomerases: Conversion of gyrase to topoisomerase IV

2007 - Evolution, Adaptation, and Supercoiling (I think this is not so relevant, that it's about the role of supercoiling in evolution rather than the evolution of supercoiling itself)

2002 - Kinetoplast DNA Network: Evolution of an Improbable Structure (A sidetrack - kDNA topology seems to be even more complicated, and corresponding more complex to replicate)

1999 - DNA Supercoiling and Temperature Adaptation: A Clue to Early Diversification of Life? (Not so recent, and a sidetrack, but v. interesting. Many subsequent articles exist on supercoiling differences in hyperthermophiles and the evolutionary relevance)

 

[Skeptical]

a few fossils certainly dont talk to the thousands of molecular and macro changes that would had to occur to take somethign out of the sea!
not to mention lots of this would simply have to co ordinated by a blind process for the organism to survive at all.

The fossil record cannot reveal minor molecular changes. However, it is a lot more than "a few fossils". There are numerous evolutionary lines revealed in exquisite detail by the fossil record. The dinosaur to bird fossil record, for example, now contains numerous intermediates.

The fish to amphibian record is not too bad, either. There are clear cut intermediate forms which show the overall pattern of evolutionary change across this line.

If your interest is molecular biology, then sure - the fossil record cannot reveal the detail. Science does not always reveal everything.

 

[Zenithar66]

Reply

The fossil record cannot reveal minor molecular changes. However, it is a lot more than "a few fossils". There are numerous evolutionary lines revealed in exquisite detail by the fossil record. The dinosaur to bird fossil record, for example, now contains numerous intermediates.

The fish to amphibian record is not too bad, either. There are clear cut intermediate forms which show the overall pattern of evolutionary change across this line.

If your interest is molecular biology, then sure - the fossil record cannot reveal the detail. Science does not always reveal everything.

firstly, I have no real main interest, I study many subjects but i admit i am particularly interseted in microbiology at the moment, if all these theists of the modern world would stop talking about miracles as though they are something that happened in the past, all they need to do is look through a molecualr biolgoy textbook, thats where the true miracles are!!

oh, and just so you know the bird dinosaur is HOTLY disputed and infact to my knowledge there was a 2009 study(I'll go try to find it now for you and link you up) that basically closed the case..

as i say, a few fossils prove nothing, and when you apply that to the birds and dinosaurs, we realise that we can't see the enourmous and frankly mind boggling changes taht would have to occur to the breathign apparatus to attain the birds uniqe system, not to mention the cold bloodednes and many thousnads of changes in geenral.

No, for me the fossil records show up one thing, that lifeforms existed in the past, changed over time(not in all cases of course) and are highly discontinous...

we simply cannot look to the fossil record to prove anything other then change over time..and certainly cant draw absolutes from it!

you cant prove evoulutions mechanisms with fossils, therefore fossils are meaningless unless evolutions mechanisms are proven to be up to the task of creating natures disturbingly beautiful adaptions...

 

[Skeptical]

as i say, a few fossils prove nothing, and when you apply that to the birds and dinosaurs, we realise that we can't see the enourmous and frankly mind boggling changes taht would have to occur to the breathign apparatus to attain the birds uniqe system, not to mention the cold bloodednes and many thousnads of changes in geenral.

No, for me the fossil records show up one thing, that lifeforms existed in the past, changed over time(not in all cases of course) and are highly discontinous...

A lot of the changes for bird to dinosaur appear to be preadaptations.
There is some evidence that certain dinosaurs had a breathing system very similar to modern birds before the dinosaur to bird evolution began.

In the same way, there are now numerous dinosaur fossils which clearly had feathers. Usually not flight feathers. While these were probably for adornment, the primary function is probably thermal insulation, which strongly implies they were warm blooded.

Some other features, though, evolved only after the first bird-like creatures evolved. For example : the loss of teeth and evolution of the bird beak. The loss of the claws on the fore limbs. The development of a sternum ridge to provide attachment for strong flight muscles etc.

The classic fossil in this line is Archaeopteryx. However, this beast was a dinosaur. A bird-like dinosaur to be sure, with flight feathers. But it had teeth, claws, and no sternum ridge. The first true birds came later.

 

[Walter L. Wagner]

you cant prove evoulutions mechanisms with fossils, therefore fossils are meaningless unless evolutions mechanisms are proven to be up to the task of creating natures disturbingly beautiful adaptions...

Actually, fossils are good indicators of where to look in the genetic materials of modern creatures. For example, the changes over time in fish, in which the fore-fins become modified to support the fish in being able to raise its head out of the water, followed by subsequent fossils of 'fish' that have bones in their fins that are homologous with vertebrate fore-limb bones, suggests that one should look to the genetic mechanisms for fish-fins as precursor mechanisms for vertebrate fore-limbs, etc.

A classic example is when certain adaptations are lost. The change over time in developing teeth, which are present in fish and vertebrates with similar genetic mechanisms, was not lost in the modern birds (and was present in Archaeopteryx; i.e. that 'bird' had teeth). Rather, a single/few hormones are inactivated, derailing the teeth development in birds. If that hormone is artificially added, the teeth-development occurs, giving birds with teeth on their beaks.

Fossils can be extremely suggestive, therefore, as to what to look for in microbiology, as there are remnant genetics still present, though no longer expressed, in modern species in many other areas of development, in which fossils can be an indication of where to look in extant species' genetic mechanisms.

The incorporation of viral DNA when the entire species becomes infected with a retrovirus, with a subsequent modification into new usages, is another area of strong interest in evolution. We've had many threads along those lines, and you might wish to do further reading before making your pronouncements as to the usefulness of fossils, etc. (I'm thinking of the retrovirus that assists in mammalian placental development, but there are about a dozen others identified).

 

[Zenithar66]

reply

A lot of the changes for bird to dinosaur appear to be preadaptations.
There is some evidence that certain dinosaurs had a breathing system very similar to modern birds before the dinosaur to bird evolution began.

In the same way, there are now numerous dinosaur fossils which clearly had feathers. Usually not flight feathers. While these were probably for adornment, the primary function is probably thermal insulation, which strongly implies they were warm blooded.

Some other features, though, evolved only after the first bird-like creatures evolved. For example : the loss of teeth and evolution of the bird beak. The loss of the claws on the fore limbs. The development of a sternum ridge to provide attachment for strong flight muscles etc.

The classic fossil in this line is Archaeopteryx. However, this beast was a dinosaur. A bird-like dinosaur to be sure, with flight feathers. But it had teeth, claws, and no sternum ridge. The first true birds came later.

actually the evidence for the breathing system is HOTLY disputed also, and its cetainly not absolute. They found certain therapods with spaces in there thoraric cavity that MAY have had airsacs, but again this is disputed by others and we cant see the lungs anymore so we may never know.
you see, a birds lungs dont contract or use a diaphram!!! try getting a fossil to show you this mind numbing transition.


as to your claim about feathers, they are not "clearly" feathers at all..
many scientist dispute this and others flat out refuse it saying it is actaully is collegen fibrers that are beign mistaken for feathers since collegn is most likely to be perserved..

of course then you have the issue of the wing, the eyes and the complimentry changes in cerrebellum that simply have to co evolve with any new usable trait! it gets worse the more you look at it..

I will admit that there are some strking similiarites between the species..
but very often in nautre this is the case, its called convergent evolution.

keep an open mind!

 

[Mr MacGillivray]

Why are we still discussing this? There are extant fish species that have a range from fully amphibious to lower degree of amphibious.

If extant fish can be amphibious, why couldn't they be in the past?

Or are we denying the present also.