... i find it difficult to believe that any strand formed by fluke ...

For those with problems about how DNA came about, I suggest they tune out the fairies in their heads, turn off The 700 Club, shut down Answers in Genesis, pop that Ken Ham DVD out of your player, and read a book written by an actual scientist. 

In metaphor-speak: Admitting you can’t understand women is not proof they don’t, in all their glorious complexity, exist.

Was born in 1948, I was 21.

Admitting you can’t understand women is not proof they don’t, in all their glorious complexity, exist.

What in all of heaven could’ve promted her to go,
After such a triumph as the ball?
What could’ve depressed her;
What could’ve possessed her?
I cannot understand the wretch at all.

Women are irrational, that’s all there is to that!
There heads are full of cotton, hay, and rags!
They’re nothing but exasperating, irritating,
vacillating, calculating, agitating,
Maddening and infuriating hags!

Moses: Was born in 1948, I was 21.

Your profile says ‘58. But I guess it would make more sense to attend Woodstock at age twenty-one than eleven. 

I’m very grateful she’s a woman
And so easy to forget;
Rather like a habit
One can always break-
And yet,
I’ve grown accustomed to the trace
Of something in the air;
Accustomed to her face.

Just you wait, professor ‘Iggins!

Yea, I was a disc jockey at CKFH in Toronto doing the all night show. Worked Friday night/Saturday morning midnightr to six, got in the car and drove to New York, partied, left Sunday morning after Santana when it really started to rain and then called in sick for work Sunday night/Monday morning because I was too fucked up to go in.

LOL. From stardust and organic material to the brown acid… Hard not to love this joint. Yes, pun intended.

For those with problems about how DNA came about

A single DNA repeat unit consists of a deoxyribose sugar (or ribose in the case of RNA) attatched to 2 phosphate groups (one in this unit, the other in an adjacent unit) and an organic base which is what contains the information and holds the two strands together. In primordial conditions there may be a range of places and temperatures for things to form which could simply be mixed by weather, and the phosphate groups, being relatively simple should have no problem forming. The organic bases are a great deal more complex units, and can be categorised as the purines and pyrimidines, these are aromatic heterocycles and synthetically there are a number of ways of making them but not with anything you would expect to find in nature anyway (like alkynes) or anything you’d expect to be available without enzymes (ie diketones) and bear in mind that enzymes are made of protein, the sequence of which is determined by a DNA sequence so you would have a chicken and egg situation. It is possible that primative DNA had different simpler bases, but at some point there would have needed to be a change to how DNA is synthesised, binding to the original chain provides a way of separating the old nucleic acid monomers from the new ones, and it is even possible the old DNA was a template for a possible second type in a useful sequence but we still can’t account for how the original chain formed a usefuul sequence.

The sugar would be more difficult still, for one thing carbohydrates typically have an alcohol group on every carbon, bearing in mind it takes something as oxidised as the very rare and toxic OsO4 to create 2 adjacent OH groups simultaneously it would be difficult to percieve creating 5 on a molecule, though thera are ways and means you could account for the odd number. The other thing about sugars is they are stereochemically pure. stereochemistry, or which mirror image a tetrahedral centre is, can be controlled by certain reactions but will never be 100%, and if there is a stereochemical fault in the right part of the DNA chain you could stip it from binding to the other strand or maybe even tRNA, in addition enzymes are natures way of controlling stereochemistry, being chiral themselves they are able to bind to only one stereoisomer of substrate in a way that produces only one stereoisomer of product, but again enzymes couldn’t be around before DNA and the chemicals you may require may not be available other than to allow syn addition in the case of things like OsO4, after all synthetic chiral chemicals are often created off the back of other chiral chemicals create by life, and you have another chicken and egg, though i will say it is possible to invert steroechemistry to possibly account for some meso centres being where they are. Primitive steroechemistry could have some control on the back of metal ions and maybe chiral polymer supports, which could reasonably form naturally given the presence of the right monomer.

There is the issue of when linking these things (phasphate and base to sugar) which group you add to what OH on the sugar, there is some chemical difference but not enough for the kind of control you would need for the regular chain you would need to be useful. I am not suggesting any act of creation accounted for this, after all they would have to interact with the physical world to infulence chemistry which we don’t observe today.

Sugars, being able to open chains to aldehydes, are able to reclose chain in a way that gives a racemate of two (alpha and beta) stereoisomers, and the difference in sterochemistry (in the absence of enzymes to control such things adding to other units) could again cause a sterochemical kink or more dramatically change which OH the phosphate or base adds to.

In order to decode a DNA chain to make proteins you need tRNA, or in the primordial case maybe something more primitive, it is possible DNA was replicating in cells long before it was decoded, nethertheless the tRNA would require 3 complimentry organic bases to bind to the chain and an amino acid residue for the making of protein, now there is an issue as to how you control which amino acid associates to what base sequence, again there will be slight chemical differences but not enough for any real control.

Hi Distant Claws:  I’m certainly no expert on chemistry, but from what I’ve read, it’s been postulated that early life was RNA based (or pre-RNA) in an “RNA world” hypothesis.  Further, some believe that the complex chemistry needed for nucleotide synthesis was present at hot oceanic vents in a reducing atmosphere.  The news that RNA can act as an information transfer molecule and it’s own catalytic enzyme (ribozyme) provides evidence that early molecules could catalyze their own replication.  Other theories postulate a Protein Nucelic Acid (PNA) structure, or Threose Nucleic Acid (TNA), especially since TNA has been shown to hybridize with RNA in the laboratory.  Additionally, PNA doesn’t have phosphate groups or use ribose as its backbone, so problems with charged molecules and carbohydrate synthesis are avoided.  Because nucleic acids are readily broken down by uv light, perhaps the “deep under the sea” hypothesis would work there also, by filtering the uv rays.
Whaddya think?

SG

Hi Science Goddess

It does make sense to use some kind of peptide, being much simpler than carbohydrates they seem much more feasable to make, I read PNA binds to nucleic acids more effectively than DNA or RNA and is more stable generally so a move to RNA would probably be to do with either 1) an advantage though mutation shows up in RNA faster, being less stable, 2) a PNA may be difficult to break down afterward, afterall an amide isn’t activated to hydrolysis like a phosphoester. As for TNA we are still dealing with carbohydrate albeit shorter so easier to make, there is still the steroechemistry issue.

UV light excites electrons typically from a bonding orbital to an antibonding orbital, amide in PNA, being a stronger bond (donating N next to withdrawing c=o with lone pair in conjugation with c=o pi* and so some n=c character)needs shorter wavelength than a weaker phosphester bond (where you have two adjacent withdrawing groups), what wavelength reaches what part of earth i couldn’t tell you, though the more it must travel through, especially through a dense mixture like the ocean, makes sense that more is absorbed. UV absorptions are broad because lower energy vibrational and rotational transitions also happen using the energy from the same photon (as well as maybe some translational if wavelength isn’t a perfect match to the last decimal place, which given in infinite number of decimal places it’s infinitely unlikely to be a perfect match) anyway all i could tell you is what reaches the earth/sea probably isn’t much of the wavelength absorbed by O3 decomposition, the bonding in O=O-O is weak, conjugation equalises bond strength and there is some alpha effect.

With all these organic molecules I wonder how c-c bonds formed, if you look at krebs cycle or the oxidative decarboxylation of pyruvate, or gluconeogenesis, you notice it all seems to use CO2, however you need a carbanion, typically an enolate in nature as one of the mildest carbanions (therefore able to exist in water), to attack it, and such things already have c-c present. What’s certain is reduction must have happened but if earth can’t hold H2, if organic reducing agents are ruled out as they contain c-c which hasn’t yet formed, if main group hydrides add without redox and if metal hydrides are too unstable for water our options are limited.

P.s. i am a chemistry student, if you would like lecture notes on a particular thing please email me

DC, you may want to put an extra line break in between your paragraphs as traditional typing style doesn’t tend to translate well to the web.

Not a criticism, just a suggestion. I’ve gone back and edited your comments for readability.

Quoting Les:

DC, you may want to put an extra line break in between your paragraphs as traditional typing style doesn’t tend to translate well to the web.

Cool, will do in future. Hell as long as my points are useful to anyone wanting an extra perspective i’m not that fussed about the formatting, language, etc, and i guess legibility helps, not something that traditionally crosses my mind

DOF, Why can’t a woman be more like a man? If I forget your birthday, are you upset.

On the whole “don’t understand it” thing. Back in the 80’s I had am Acorn Electron (basically a cut down BBC B home computer: a VIC20 type of thing)(Les- No nostalgia yet)

Back in those good old days it was easy, indeed required, you knew how to program (in BASIC).  I had a program from a mag, that if you played a music tape through the IN socket, would create groovy disco light effect on the screen, affected by the music.  The guy who programmed it said he had NO IDEA how or why it worked.  If something WE MADE was a ‘black box’ what chance do we have with a complete explanation of nature?

If something WE MADE was a ‘black box’ what chance do we have with a complete explanation of nature?

Both are, in principle, explicable, and differ in this respect from God. 

Both are, in principle, explicable

Yes, but the explanation may be a lot less useful than one might expect. My standard example is good old Langton’s Ant.

It’s a very simple system and we know all its rules. Yet for all its simplicity, the system has complex emergent properties and in general, we can’t predict the system’s long-term behavior short of running it and observing what it’ll do.

We may or may not figure out all of nature’s rules at some future date. Even if we do, there are limits what we can do with such knowledge.

We may or may not figure out all of nature’s rules at some future date. Even if we do, there are limits what we can do with such knowledge

Agreed. There isn’t necessarily a way of finding laws where everything behaves the same under conditions we can’t change (since time goes forward for example), and where predictions by simple inversion may not necessarily be valid if more laws are behind the scenes than are known.

There is the possibility of the effects of two laws cancel leaving neither observed, at least not to the full extent of what those laws do. And use of some laws may well be impractical, pointless or dangerous to use.

The most basic laws of nature have no reason to be the case, everything traces back to them and they are indeed observed to be true but don’t have reason to apply with there not being anything more fundamental to explain them. The attraction between opposite charges for example has energy associated to account for observation but there is no reason why there should be this association in the first place, therefore no reason for charges to attract and no reason why atoms should hold onto electrons. Similarly light provides one means to distribute energy statistically but there is no reason why light should be able to carry energy, especially since it has no momentum. Indeed deeper still there is no reason why it should require energy and time to move mass, therefore no reason why movement should not be instant and no reason why kinetic energy should exist as a consequence, and without that a hypothetical chemical couldn’t absorb any light as it couldn’t match wavelength to an infinite number of decimal places and the normal unquantised pool for the difference (translational energy) wouldn’t exist

And if Gödel’s Incompleteness Theorems apply outside of the realm of formal logic, we face a brick wall to run into. Of course, when applied to theology, these theorems have interesting ramifications, too.

Hey, DC. That was cool; I even understood it. 

Elwed, thanks for the pointer.
Kurt Gödel sounds like interesting; Albert Einstein said: that “his own work no longer meant much, that he came to the Institute merely…to have the privilege of walking home with Gödel”.

I suppose when you’re that smart you’re allowed to be slightly mad too.

Late in 1977, Adele became incapacitated due to illness and so could no longer cook for Gödel. Due to his paranoia, he refused to eat any food at all and thus died of “malnutrition and inanition caused by personality disturbance” in Princeton Hospital on January 14, 1978. He weighed 65 pounds.

Not being a mathmatition this is out of my depth but wow, the idea that this extends to mathematics, which science and computing relies heavily on as their only way of quantifying things. I was thinking about the difference between computers and the human mind recently, computers are excellent calculators but can’t handle inexact numbers so well, whereas the mind is much less able to calculate yet can coordinate all your limbs much better than current robots, and doesn’t require exact info from your eyes, apply trigonometry, etc, almost as though it does it without much calculation, using a system other than mathematics to quantify and handle inexact data efficiently.

The mind is able to do things computers can’t, you can decide where to go, but you don’t need to think about the exact position, it has consciousness, which there is no obvious way to program, it has an inexact memory that is able to lose information but later retrieve it, it holds different amounts of information at different levels of consiousness and makes decisions on what has been retrieved despite sometimes holding more, changing it’s mind as more is retrieved, it is able to identify objects from an image without even needing a well defined border in the case of blurry eyesight, it can identify the words of a voice it has never heard, identify different sounds from the mush of frequencies that come in and even blank some of them out, and it is it’s own interpreter of information.

Mathematics can attempt to allow error using exactly and arbitarily defined error bars, student’s T values, etc, but it is still trying to be exact about being inexact.

Neither theology or science completely describes the world alone as they are, and neither the laws of physics or god ultimately have a reason to exist, and may (or may not) result from each other to do so, if this or the laws of physics are equally fundamental and can’t exist alone we have a cyclic dependance and maybe a complete answer, with the big bang happening at the point where these laws suddenly came to exist.

It is a difficult concept that more than one thing can be equally dependant to exist as they must have happened simultaneously and we are not at the point at finding this dependance, it isn’t something we can test as we can’t turn off a law, but it’s still possible even when paired that there is no fundamental reason for the laws to form unless it is somehow impossible for them not to, i can’t put formation of laws down to probability without parameters.

I will study up on Gödel’s Incompleteness Theorems with great curiosity because this looks like the next step in figuring it out

Quoting LuckyJohn19

Hey, DC. That was cool; I even understood it.

Thankyou, the more lectures you sit through the more you realise nobody knows what’s going on

I suppose when you’re that smart you’re allowed to be slightly mad too.

As far as I can gather it’s part of the deal, quite tragic though, people like Wallace Carothers and Ludwig Boltzmann made great contributions to my field but were severely depressed, also Alan Turing comes to mind, perhaps their minds go into overdrive and the only thing for it to do is self-destruct, and/or perhaps they have things like aspergers that causes a different perception of the world that whilst helping their research doesn’t conform to society, making them depressed that way. These are only the famous cases, credit for research doesn’t always go where it should and some may simply be born too late for their abilities to help.

I have to say though that even in science there aren’t that many geniuses, nowadays you get students who can remember lots and work hard but couldn’t create this stuff themselves or necessarily understand it, i have known people with incredible parrot fashion memory and grim resolve, and the modern degree bombards you with memorisable content and coursework that drowns out creativity.

People with autistic spectrum disorders generally appear to have less commitment because their emotions can generally fire more strongly (this amplifies isolation feelings) despite not showing it, such people are as a result being driven away from science, and many don’t work at all because they tend to be highly specialised.

Those that commit suicide are willing to give it all up for the possibility of relief despite the gamble of hell, beyond a point i guess you just want out, that’s why i believe organisations like the samaritons are important, regular psychologists generally havn’t been through that kind of thing and don’t really understand it, it’s not something you can just read about and understand, they just tick boxes for criteria and perscribe pills without dealing with the real issues that don’t necessarily always have an obvious trigger and so has no real answer, sufferers need things explained like the hole it leaves in families with distress and confusion, that life is tempory anyway so hell you may as well at least hang around to see what happens because you’re a long time dead, that there is always escapism in video games and books, that physical needs outweigh psychological ones and being tired enough the same things aren’t on your mind, and that keeping occupied generally can break the patern

Neither theology or science completely describes the world alone as they are

Scientists describe the world that is to best of their abilities; theologians merely describe the world that they would like to be.

There are probably questions that science will never answer and that’s okay with me. If you know all answers, what’s the point in continued existence?

and neither the laws of physics or god ultimately have a reason to exist, and may (or may not) result from each other to do so, if this or the laws of physics are equally fundamental and can’t exist alone we have a cyclic dependance and maybe a complete answer, with the big bang happening at the point where these laws suddenly came to exist.

Duuuuuude!  I mean like, woah!!!

Seriously, how would we know if the laws of physics ultimately have a reason to exist?  We have our hands full finding out what they are.  As for the laws of god, if such there be, they do not belong in the same sentence.  There is verifiable evidence of one, the other is pretty much made up.

Either that, or religion x got it right and religion y got it wrong, and again we have no way in the observabable, calculable universe to tell which is which.

You try to capture anything reproducible, measureable, and verifiable about religion and all you get is a lecture on faith.  As for what we’d do if science ever did figure everything out (don’t hold your breath), I feel pretty comfortable saying “we’ll figure it out when we get there.”

Distant Claws wrote:

...regular psychologists generally havn’t been through that kind of thing and don’t really understand it…

Why do you say that? Sometimes people who have gone through unusual trials and tribulations go on to become licensed psychologists precisely because they have experienced tremendous pain and suffering for themselves. I’ve gone to a therapist who attempted several times to end his life before going back to school and regaining control over himself. At least from personal experience I’ve found that the best therapists usually aren’t the ones who have just sailed through life.

...they just tick boxes for criteria and perscribe pills without dealing with the real issues that don’t necessarily always have an obvious trigger and so has no real answer…

What is this evaluation based on? Certainly this is what the “bad” doctors do, but I would hope that any therapist or psychiatrist worth his/her salt would attempt to tackle “the real issues.” For that matter, what even are “the real issues?”

...physical needs outweigh psychological ones…

If you mean basic physical needs such as oxygen and nutrition, you’d be correct. At least most of the time.

If you mean basic physical needs such as oxygen and nutrition, you’d be correct. At least most of the time.

Yes.  Though Thom Hartman, who despite his being somewhat new-agey I do like a lot, proposed that Maslow left off his pyramid a “need for aliveness” and there certainly is some evidence for that.

I never quite trust the logic of someone who doesn’t know what puncutation and especially a period, is for.
Your picky scribe;
Allan W Janssen