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  Topic: Abiogenesis discussion thread, No trolls please, we're adults< Next Oldest | Next Newest >  
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Dec. 17 2006,22:24   

Quote (Louis @ Dec. 17 2006,18:07)
Skeptic,

You thought I was GoP? Ow that hurts. Any serious contributions or are you simply befouling the thread because you've been asked not to? A bit childish no? Smarmy faux compliments irritate me anyway.

Nothing so sinister.  I was scrolling through and I saw the pretty pictures and the long post and GoP popped into my head.  :D

A quick second look revealed the truth and I had a little chuckle which I thought I'd share with you.  No need to threaten censorship as you see.

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 18 2006,03:30   

Skeptic,

I know what you meant re GoP. I was being humourous. Mi apologias for not being clear enough

Not censorship by any stretch of the imagination. Asking for some irrelevant posts to be moved to the bathroom wall isn't censorship, it's porting irrelevant garbage to the relevant place. Make your last post your finalno science poston this thread please. And I have no power or authority here, I can only ask Steve or Wes to do this. They can, and quite probably will, say no.

I just have a fervent hope that on one thread we can focus on, ya know, the science rather than the trolling. Any chance? Any at all? Please. I have asked very nicely several times. By the very virtue of having this conversation we're doing exactly what I hoped we wouldn't.

Louis

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Bye.

  
Alan Fox



Posts: 1365
Joined: Aug. 2005

(Permalink) Posted: Dec. 18 2006,04:08   

Quote (Louis @ Dec. 17 2006,12:16)
Alan,

Colour me extremely confused and/or shocked.

Are you saying that the witterings of the IDCists are valid when applied to abiogenesis due to your/their personal incredulity?

If you're not, please forgive me for even beginning to insinuate that you were! I shall say 10 "Hail Dawkins" and beat myself with a copy of "The Origin of Species" for a month.

If you are.......wuh wuh wuh wuh....gibber. Please explain.

Cheers

Louis

No, just observing that if the mousetrap argument had been applied to abiogenesis, it would have been less easy to refute. I was just remarking that there is quite a narrow window for abiogenesis to occur between a cool and wet enough earth and the first evidence of stromatolites. I can see that it did happen. I can believe that it was a natural process, but I doubt we will ever know how it happened. So room for "Goddidit" for those that need that hypothesis.

I am far from up-to-speed on the latest theories and developments, anyway. Robert Shapiro sold me the idea that abiogenesis is a much tougher nut to crack than evolution; he is also doubtful that "RNA world" will turn out to be a succesful hypothesis.

  
deadman_932



Posts: 3094
Joined: May 2006

(Permalink) Posted: Dec. 18 2006,04:47   

For those that have access to book/journal stacks in uni's or colleges:

Osawa, Syozo, "Evolution of the Genetic Code"  (Oxford University Press, Oxford, 1995). mechanisms of molecular evolution of the genetic code.

“Contribution of Cosmic Rays, Radiation, Lightning and Geothermal Heat to Prebiotic Synthesis on the Primitive Earth” In: The Role of Radiation in the Origin and Evolution of Life (Akaboshi, M., Fujii, N. & Navarro-Gonzalez, R. (Eds.)) (Kyoto University Press, Kyoto), pp. 9-24.

Terada, R., Imai, E., Honda, H., Hatori, K. & Matsuno, K., 1999 “Fixation of Carbon Dioxide in Hydrothermal Environments: Synthesis of Formic and Acetic Acids” Viva Origino 27, 197-208.

Matsuno,Koichiro:  “Submarine Hydrothermal Vents Preparing the Emergence of Life and Likelihood in the Laboratory Experiments?” Genetics - Biological Science 53-7, 6-7

Imai, E., Honda, H., Hatori, K. & Matsuno, K., 1999. “Autocatalytic Synthesis of Oligoglycine in a Simulated Submarine Hydrothermal System” Origins Life Evol. Bioshere 29, 249-259.

Much of Matsuno's work is available for online reading here, too: http://bio.nagaokaut.ac.jp/~matsuno/preprint.html

For some online reading:
http://www.gla.ac.uk/Project/originoflife/index.htm
http://www.origins.rpi.edu/research.html
http://www.resa.net/nasa/origins_life.htm
http://www.lcb.uu.se/~dave/publications.html
http://www.chemistry.ucsc.edu/Projects/origin/home.html

http://www.astrobiology.com/
http://adsabs.harvard.edu/cgi-bin....be00373 article on the stability of aminos in space (hit pdf link) such articles can be found in http://www.adsabs.harvard.edu/ , including lots of interesting stuff on chirality of prebiotic molecules, or http://adsabs.harvard.edu/cgi-bin....format=  (on "The Astrobiology of Nucleobases") good stuff , Maynard.

http://mcb.harvard.edu/BioLinks.html (for dealing with bio terms)

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deadman_932



Posts: 3094
Joined: May 2006

(Permalink) Posted: Dec. 18 2006,05:50   

I found these in another text file I had on abiogenesis/origins of life stuff:

Martin W, Russell MJ. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc Lond B Biol Sci. 2003;358:59–85 http://www.gla.ac.uk/project....ell.pdf

Other origin of life PDF's available at this site I had mentioned in previous post: http://www.gla.ac.uk/projects/originoflife/html/2001/pdf_articles.htm

Mulkidjanian, A., et al (2003) Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. Evol Biol. 2003; 3: 12. Published online at http://www.pubmedcentral.nih.gov/article....ols=bot   ***see also the reference list cited in this article

Montmorillionite Clays and catalysis
http://www.ncbi.nlm.nih.gov/entrez....2458736 and http://www.ncbi.nlm.nih.gov/entrez....5570708
Clays seem pretty interesting in terms of autocatalysis and early cell formation, etc.

By the way, the Santa Fe Institute got a nice fat grant to study Life Origins last year, in conjunction with some other Uni's  
Quote
October 18, 2005 -- The Directorate for Biological Sciences at the National Science Foundation (NSF) announced that the Santa Fe Institute (SFI)--along with collaborating institutions George Mason University, University of Colorado, University of Illinois at Urbana-Champaign, Arizona State, and Carnegie Institution of Washington--has been awarded a five-year Frontiers in Integrative Biological Research (FIBR) grant for their joint project, "The Emergence of Life: from Geochemistry to the Genetic Code."
and some links to relevant papers can be found at : http://www.googlesyndicatedsearch.com/u....afe.edu

Note: If anyone hates PDF's as much as I do, and the slowness of Adobe Acrobat ( yeah, I know you can strip out a bunch of crap it loads , but it's still cumbersome) --get  the free Foxit pdf reader at http://www.foxitsoftware.com/pdf/rd_intro.php

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AtBC Award for Thoroughness in the Face of Creationism

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 18 2006,06:02   

Alan,

{thwack} Our Dawkins Who Art Mostly in Oxford, Richard be thy name...{thwack}

Ok enough funny.

I'd agree that in certain senses abiogenesis is a tougher nut to crack than evolutionary biology. But not in all senses.The senses in which I think this is the case are due to things like time taken for certain evolutionary processes etc. We can synthesise self replicating molecules quicker than nature can evolve them for example, these are things accomplishable in a human lifespan. So in some senses abiogenesis is an easier nut to crack.

However, as I allude to above unlike evolutionary biology in abiogenesis research we simply don't have the fossils in the same sense. We have a different problem, instead of lacking fossil chemicals in their entirety, we are drowned by huge amounts of chemical noise from which a signal is almost impossible to distinguish. We also have a really unique situation in that we have a really good idea of what sorts of chemicals were available on early earth and in space, and we have a really good idea of what is available now. We have a comparitively poor idea about which paths were taken between the two points! We do however have many great ideas about which paths COULD have been taken.

If you consider how complex a topic we're dealing with that's a pretty advanced state of knowledge. Granted it isn't a step by step process of what definitely, but are you sure you're not asking for something that you cannot get in order to avail yourself of the "poof goddidit" loophole? After all, we don't have a step by step process of the relationship between humans and out last common ancestor with chimps. Does this provide a "goddidit" loophole? Of course not! We don't actually need the step by step "photograph" of each link, the relatonship is demonstrated by different evidence. The DNA, fingerprints, footprints, fibre traces etc left by a burglar demonstrate his or her presence in the burgled domicile as well (in fact vastly better) than a CCTV picture. The emotional appeal of a CCTV picture is a different beast, but it is of lesser evidenciary significance.

I'm curious as to why you seem to need to single out abiogenesis as more friendly to the Beheian mousetrap ideas. More friendly in your personal estimation perhaps, but very far from being actually more friendly.

Cheers

Louis

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Bye.

  
Louis



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(Permalink) Posted: Dec. 18 2006,06:06   

Deadman,

Thanks very much indeed for all of that. Not least the pdf reader alternative!

Louis

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Bye.

  
Mike PSS



Posts: 428
Joined: Sep. 2006

(Permalink) Posted: Dec. 18 2006,08:14   

Quote (Louis @ Dec. 17 2006,18:08)
Mike PSS,

   
Quote
Has there been any agreement from the researchers involved about the environmental conditions at the time of abiogenesis?

{snip}......{/snip}

If not, shouldn't finding this out be condition 0) for your tract.


I honestly don't know if there has been "agreement", depending on what one means by agreement. Are there a variety of plausible evidence based scenarios, one of which has yet to be 100% settled on by all relevant experts everywhere? Yes. So as for agreement the answer is yes and no!

Should this be condition 0) for my "tract"?

[Outraged John Cleese voice]

Well the first thought is "tract"? I'm fucking Jack Chick now am I? Tract? Kiss my heavily polished not particularly black arse! Tract. Fuck off.

[/Outraged John Cleese voice]


Ok so I'm kidding about, don't take the above to heart or in any way seriously.

What I think the question is is this:

"Is a complete description of the environmental conditions for the early earth, when we think abiogenesis occured, available?"

Ahhhh... so many ways to respond to Mr. Cleese.  Shall it be classic MP?  Some of the stage work?  Films (I was thinking Kevin Klinesque at first since the psedo-psychological rantings could produce some chuckles).  Naw, I choose the simple route.

[Normal Manuel voice]
"Qué?"
[/Normal Manuel voice]

*****************************
My comment, although sparse in detail, is angled more on the 'energy pump' aspects of any first self-replication survivor.  With your references and others I see a few alternatives for the energy source, and eventual energy stream, for our first bugs.

1.  Sulfide/Sulfate energy source.  Originating source from the hydrothermal vents that have most likely existed on earth since the oceans first formed.
(O.K. Sulphur for you East Atlantists, I'll also state that Al-U-Min-E-Um is more correct but becoming more archaic.  Color....   errrrr  Colour me surprised that you cling on to this usage as "MORE" correct)

2.  Water surface energy source, maybe a CO2 or hydrocarbon source.

3.  Specific catalysis products in some specific area.  This source could be a vent from a large deposit of hydrides (H2 product is possible) or other such chemistry where a catalysis starts the breakdown of an older geologic deposit after some specific geologic change (uplift exposure to air/rain, fold exposure to water, volcanism through formerly stable areas, metamorphic change, etc...).

The first 'energy pump' piece of abiogenesis would have to be a simple system and the self-replicator may have located itself in an area where unstable (read higher-energy) sources of chemicals occur so that the first 'energy pump' consisted of simple autocatalytic (or catalytic, see below) one-step reaction.

Another aspect of these conditions is the availability of catalysts.  Although autocatalytic processes are an easier condition, a catalytic process may be necessary in these early conditions.  As Deadman referenced...  
Quote
Montmorillionite Clays and catalysis
http://www.ncbi.nlm.nih.gov/entrez....2458736 and http://www.ncbi.nlm.nih.gov/entrez....5570708
Clays seem pretty interesting in terms of autocatalysis and early cell formation, etc.

Deadman, just had one correction on your comment.  Autocatalysis implies no external factors.  The presence of clays (Fe, Mg, Mn, etc...) would be external catalysis only.
Anyway, the first replicator could use an available catalytic source (say a clay ball) located near a source of higher-energy molecules (list above) to source its energy for life.

I'll become more verbose on this thread to bore the he11 out of everyone.

Mike PSS

I'm a BSc chemical engineer and spent the last 10 years working in industrial production.  My first seven was with phosphate fertilizer manufacture.  Interesting process;
-first making 8000 tons per day (tpd) of sulfuric acid by burning liquid sulphur (SO2) then catalysing to SO3 then scrubbing to H2SO4 (98%).
-then using all that sulfuric acid to attack 12,000 tpd of phosphate ore (the drag lines at the mines are massive) becoming phosphoric acid and gypsum.
-combine the phosphoric acid with liquid ammonia and you get 7,500 tpd of a high quality Di-ammonium Phosphate (18-46-0) or Mono-ammonium Phosphate (10-50-0).
Big equipment, big material balances and big energy swings in every process.  Lots of fun after the lab scale processes taught in school.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Dec. 18 2006,09:43   

abiogenesis is a much tougher nut to crack in this sense:

Behe's whole argument, with or without the mousetrap, is a God-of-the-gaps argument. In terms of the evolution of various complex structures from less complex precursors, he's already said that he'll accept nothing less than a mutation-by-mutation account of how it happened. Which is ridiculous, of course, and at odds with what he wrote in "Darwin's Black Box", the gist of which - as I recall, anyway; I consider it not worth my while to go back and check - is that no plausible paths are even conceivable. So, just like the transitional fossil charade, where any series of N transitional fossils between point A and point B implies N+1 gaps, any awake reader can see that Behe is just pre-moving the goalposts. So the gaps in which he's trying to hide God get to be elastic to the point of meaninglessness.

Abiogenesis is different, though. There is no point A, so the gap in which God resides is much more spacious, and there's not the same sense that it's getting smaller with every new issue of Nature.

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deadman_932



Posts: 3094
Joined: May 2006

(Permalink) Posted: Dec. 18 2006,12:06   

Hah, yeah, you're right, Mike -- I had autocatalysis on the brain after looking through some of the Santa Fe material I have -- I should have simply said "catalysis."

Per Russel on Behe's (and Dembski's) facile rewriting of claims -- Behe and Dembski have both not merely moved the goalposts, but they've essentially put wheels on them. Classic God-of-the-Gappism. And yeah, he does say what you stated, concerning multiple systems, pp. 39-50 and onward of "Black Box."
See also http://www.don-lindsay-archive.org/creation/behe.html
and section 4.2 of http://www.talkorigins.org/design/faqs/nfl/#defense by Richard Wein

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"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Dec. 18 2006,17:47   

Quote (Louis @ Dec. 17 2006,18:44)
esp on counter creationism and **Viking Piss. **

Tee hee --- those who came late to this party are probably scratching their heads wondering that the #### you're talking about.   ;)

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www.RedandBlackPublishers.com

  
Alan Fox



Posts: 1365
Joined: Aug. 2005

(Permalink) Posted: Dec. 21 2006,04:59   

Quote
I'm curious as to why you seem to need to single out abiogenesis as more friendly to the Beheian mousetrap ideas. More friendly in your personal estimation perhaps, but very far from being actually more friendly.


Hi Louis

Been too busy to respond, lately. In case the thread is not yet moribund:

Friendly is not what I feel towards Behe or his mousetrap. Russell puts it neatly.

Say a Mars probe was able to recover and bring back soil samples.

Resulting analysis may show:

1) No evidence of life (I know the "one white crow" argument, it was a big sample :) )

2) Evidence of lifeforms, carbon-based, DNA, proteins, same chirality.

3) Evidence of lifeforms, like nothing on Earth.

Would I be right in concluding from 1, Life is a rare, maybe unique event. We may never explain its origin. From 2, panspermia looks a strong possibility and abiogenesis could still be a unique event that occurred elsewhere than on Earth. From 3, we are not alone and the Universe is teeming with life.

I also find the thermal vent hypothesis more compelling than a warm pond. You have the high temperatures, minerals and nutrients close to cold therefore stabilising water with convection currents quickly moving chemicals away from the "manufacturing" hot-spots, preventing them from quickly breaking down again.

  
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Dec. 21 2006,15:59   

I have to go out of my way to thank Louis once again for this thread, and I guess GoP for the original idea.  Here's my reading list for the holidays:

Aquagenesis - Ellis
Biocosm - Gardner
The Plausibility of Life - Kirschner and Gerhart
The Spark of Life - Wills and Bada
Independent Birth of Organisms - Senepathy

I'll check in after the holidays and add my comment of substance, til then Happy Holidays, Merry Christmas, Happy Hanakkah, Happy Boxing Day, Happy New Year and for our resident atheists Happy Anti-Christmas.

Talk to you all next year.

  
stephenWells



Posts: 127
Joined: April 2006

(Permalink) Posted: Dec. 21 2006,16:05   

Quote (Mike PSS @ Dec. 18 2006,08:14)
(O.K. Sulphur for you East Atlantists, I'll also state that Al-U-Min-E-Um is more correct but becoming more archaic.  Color....   errrrr  Colour me surprised that you cling on to this usage as "MORE" correct)

Oddly, that element was originally called alumium (cf. sodium, potassium), aluminum is a more easily pronounced Americanism, aluminium is then a back-formation from that to recover the -ium ending. So, the ^^%^% with it, everyone's wrong :)

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 22 2006,09:51   

Alan,

My bad for being confused.

I think in each of your three examples, as you note, the sample size is too small to make "global" or "universal" claims about the feasibility or otherwise of abiogenesis. They would however all be fascinating data points in "local" abiogenesis research.

I'm really cautious about making massive "universal" inferences from limited sets of data. For example the idea of universal and local homogeneity of physical processes/"laws" is based on a huge series of observations from pretty much every field of human enquiry. Observations of life/lack of life on Mars and its comparison to earthly life are a miniscule subset of the possible data. Finding life on Mars would be fascinating and may tell us a huge amount about local abiogenesis (or not).

The comment of Russell's about there being no point A baffles me to to be honest. The only reason that this gap appears to be unchanged by every issue of Nature is that chemists rarely publish in Nature! Ok so that's not a serious point at all!

What I am really confused about is this "no point A" stuff. Maybe it's my dumb chemist brain but I see one HELLOVA lot of point As. Perhaps you and Russell could expand on this for me because I'm confused. (Possibly due to current state of crippling hangover but I digress).

Louis

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Bye.

  
Louis



Posts: 6436
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(Permalink) Posted: Dec. 22 2006,11:18   

Mike PSS,

Re: hydrothermal vent and Fe/S chem as an early source of energy for early organisms, yup absolutely, a great candidate. And Fe/S chemistry has some interesting facets that might be really key. The lability of some S based ligands in Fe complexes for example.

I guess I'm thinking vastly simpler in terms of what the Ur-replicator might have been. I don't see them needing an "external" energy source probably because I'm thinking of them as simple chemical reactions in the sense described in my kinetics post previously. I.e. the enthalpy difference between reactants and product is the driving force for reaction, and the fact that the reaction is catalysed/autocatalysed lowers the activation energy and favours one reaction pathway over others.

This is why I am asking for people's ideas of orders of events. Because I don't see that a self replicating molecular system is much of a hurdle at all. The combination of this with encapsulation and that system then "repoducing" is a different bag. My guess is that this is a really tricky step and absolutely requires the soort of energy pumps you describe. The templating of clays/minerals is I agree a really key to either a self replicating system (although it's not necessary, but could be very helpful) and/or encapsulating a chemical system. In fact were I to make a guess it would be that encapsulation happened early in abiogenesis because a relatively "high tech" replicating system would be positively hampered by encapsulation.

So my first general guess is roughly thus:

1) A simple self replicating system develops which is either initially autocatalytic or templated/catalysed in some fashion.

If templated/catalysed the template or catalyst must be capable of being encapsulated with the self replicating system (this is why I am a fan of polymeric carbohydrates as structures for templation, and guess what, these are "simple" polymers, "spring loaded" to polymerise at the anomeric position, the monomers are found in space/abiotic systems and their formation is diastereoselective).

2) This simple replicating system is then encapsulated in some fashion (micelles, mineral absorption etc). The barrier/walls of the capsule must be at least semi permeable and must permit the influx of reactants (this isn't as hard as it sounds. Think osmosis)

3) The encapsulated replicating system is subject to natural selection (more stable/fecund etc systems persist at the expense of crappier ones). This is the stage I think your energy pump idea is really valuable. Systems which can more efficiently use the resources around them, who's kinetics are simple/robust enough to take advantage of external energy sources will tend to work better.

Whaddya think?

Louis

P.S. I speeek-ah Eeenglish verrry goood. I-ah learn eeet from-ah boook.

P.P.S. Sulfur and aluminium are the IUPAC standards. Even us Brits behave ourselves when it comes to IUPAC!

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Bye.

  
Mike PSS



Posts: 428
Joined: Sep. 2006

(Permalink) Posted: Dec. 22 2006,13:32   

Louis,
This is the point I need to do some more reading from the assigned list.  The details of the next point of discussion start to get fuzzy in my mind because I lose sight of everything going on at once.  Holiday reading I guess.

Sticking to the thermal vent environment might be helpful for the moment.

My initial thoughts about your 1) 2) 3) scenario are:

1)  Plausible for carbs.  Easy to polymerise and easy to find in the environment we're talking about.  I think the polymer chemistry in this step is what will set up step 2) as a first Ur-replicator.

2)  The polymerisation products in step 1) may form the encapsulation layer here.  A branched polymer or co-polymer is an option to consider for incorporation within the encapsulation layer with one branch backbone adapting to the miscelle barrier and the other branch backbone internal and/or external to the barrier (the first resemblance of an interbarrier receptor).  As new variants of polymer chains are included in the miscelle then new chemical reactive functions may appear depending on backbone structure and chain endings.  Now we would have a system incorporating the full variety of organic chemistry in the vent environment.

3)  The energy pump system is probably an Ionic Pump type found in cell functions today.  The Ion source is produced in the vent or the exposed Fe catalyst source.  One item I thought of is that the miscelle formation would change the water conditions inside the miscelle formed in 2) so that the Ionic Pump system has a greater energy release or different product mix (maybe moving the equilibrium or solubility of the products one way or the other).  The Ionic Pump system would also have to maintain the internal miscelle conditions so that this reaction could be sustained.

Just musings for now.  I'll see how good this holds up in the literature.

Mike PSS

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Dec. 22 2006,13:35   

Quote
The comment of Russell's about there being no point A baffles me to to be honest. The only reason that this gap appears to be unchanged by every issue of Nature is that chemists rarely publish in Nature! Ok so that's not a serious point at all!

What I am really confused about is this "no point A" stuff.
Nothing all that profound, really.

I'm just noting that evolution is all about getting from one form to another by "descent with modification". So it's no big deal (unless your mind is stunted by religious indoctrination) to get from Australopithecus to Homo, or even from worms to chickens. In each case the "point A" is pretty well known and understood.

But for abiogenesis, "point A" is nonliving, nonreproducing, precursors of unknown composition, in an unknown environment. And "point B", the bacteria-like creatures reflected in the earliest fossil stromatolites (I guess that's the earliest we have, but I'm not expert or even current on this stuff), (1) is not very well known or understood itself, and (2) represents a much huger leap than any other "point A - point B" pair plausibly addressed by any real science.

It's sort of like giving a Martian detailed directions to get to the Empire State Building, starting with "Go north on 1st Avenue to 34th Street...."

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Steviepinhead



Posts: 532
Joined: Jan. 2006

(Permalink) Posted: Dec. 22 2006,15:27   

You guys have been working on this for a whole week now, and you still have no definitive result...?

And yet you Darwinists are arrogant enough to call yourselves "scientists"!

The only thing this little exercise demonstrates is that life must be complexly specified if abiogenesis can't be solved through such massive application of brainpower over such an enormous length of time...

</troll-mimickry>

  
deadman_932



Posts: 3094
Joined: May 2006

(Permalink) Posted: Dec. 22 2006,16:22   

Speaking of troll mimicry:  
Quote
The energy pump system is probably an Ionic Pump type found in cell functions today.  

YEAH I GOT YER PUMP RIGHT HERE

Just for you, Louis. Ah, memories.  :p

By the way, here's something to read : "Genesis: The Scientific Quest for Life's Origin"  by Robert Hazen, a colleague of theoretical biologist Harold Morowitz and physicist James Trefil at George Mason U. -- it has an iffy title ( at least to my taste) but it's pretty good , and it's fun, and most importantly, it's FREE. A doc. file is available here :   http://hazen.gl.ciw.edu/publica....ownload

or you can look at it in HTML online here:  http://209.85.165.104/search?....nk&cd=8

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skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Dec. 25 2006,23:38   

My holiday reading is raising more questions than it answers, which is fantastic, but I have one in particular that I keep coming back to.  I'm not sure if it falls under evolutionary biology, genetics or molecular biology but given the diversity on this board I think we've got them all covered.

My question relates to conserved genes and specifically those that are conserved in vastly different species.  Is it the commonly held assumption that these genes are just remnants that are not expressed or are they actually active genes?  I'm thinking in terms of a conserved gene similar in both single-celled organisms and higher mammals.  Would they just be latent in the mammal or are they actually expressed and participate in some basic process?  I know generalities aren't very useful but I'm just trying to get some idea if there are any trends in these cases or a consenses of thought on conserved genes.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Dec. 26 2006,03:14   

There a quite a few genes that are conserved over all domains of life, such as those involved in DNA and protein production, transcription and translation, and central metabolism. There are also a lot of genes that are used across a lot of species for different purposes, as recent analysis of the sea urchin and amoeba genomes has shown.

For those with plenty of time on their hands I highly recommend 'The principles of life' by Tibor Ganti. A good review is
here.

  
ericmurphy



Posts: 2460
Joined: Oct. 2005

(Permalink) Posted: Dec. 26 2006,15:07   

Quote (skeptic @ Dec. 25 2006,21:38)
My question relates to conserved genes and specifically those that are conserved in vastly different species.  Is it the commonly held assumption that these genes are just remnants that are not expressed or are they actually active genes?  I'm thinking in terms of a conserved gene similar in both single-celled organisms and higher mammals.  Would they just be latent in the mammal or are they actually expressed and participate in some basic process?

I can't imagine that a gene that is not expressed or that otherwise serves no function would be conserved. A functionless gene would not be subjected to selection pressure, and therefore could mutate without restriction.

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Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Dec. 26 2006,15:52   

Quote
I can't imagine that a gene that is not expressed or that otherwise serves no function would be conserved. A functionless gene would not be subjected to selection pressure, and therefore could mutate without restriction
Conversely, if a gene, or stretch of DNA sequence is conserved significantly (i.e. statistically significantly) better than "filler" like intronic sequences, or unexpressed pseudogenes, you can be pretty sure that it either has a significant function, or at least has until the most recent generations. This is one area where ToE makes useful predictions, but afdavism comes up, once again, empty-handed.

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"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 26 2006,18:14   

Quote (skeptic @ Dec. 25 2006,23:38)
My question relates to conserved genes and specifically those that are conserved in vastly different species.  Is it the commonly held assumption that these genes are just remnants that are not expressed or are they actually active genes?

There are several genes that are conserved across virtually all life, and others that are conserved across virtually all multicellular life.  In nearly every case, these are basic central "housekeeping" genes that perform the most basic and vital cell functions.  Since they work well enough to get the job done, there's not much point in changing them.  At the cellular biochemical level, all life is pretty much the same -- a banana cell isn't very different from a human cell. They all have to do the same basic biochemical tasks, and since they're all descended from each other, the simplest solution is to keep doing the same thing, over and over and over.  (It's the NON-descendents, like virii and the most primitive prokaryotes, who show different biochemistries).

As for multicellular organisms, all the really important stuff happened in the pre-Cambrian (how to make cells stick together into one body, how to form various internal layers, how to determine front from back and up from down).  Since then, multicellular life has consisted simply of minor variations on the same theme -- multicellular animals are just tubes with various numbers of things sticking out the sides.  At the basic biochemical level, a flatworm and a human simply are not that different from each other.

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skeptic



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(Permalink) Posted: Dec. 26 2006,21:11   

So essentially we're looking at a "Why reinventing the wheel" scenario?  Something that troubles me is that all the differences would then be improvements of original genes without much actual innovation.  I'm sure this must be the general case and exceptions exist.  Whatever the case I surely plan on looking into this more.

  
"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 26 2006,22:07   

Quote (skeptic @ Dec. 26 2006,21:11)
So essentially we're looking at a "Why reinventing the wheel" scenario?  Something that troubles me is that all the differences would then be improvements of original genes without much actual innovation.  I'm sure this must be the general case and exceptions exist.  Whatever the case I surely plan on looking into this more.

Actually most of the major innovations are the result of gene duplication, followed by variation in the duplicated gene.

When it comes to basic genes like HOX genes, a small change (a single duplication, for instance) can have a large effect on the final phenotype.

Or, in the case of the appearance of eukaryotes, the major innovations came from symbiosis, and weren't genetic at all.

But at the basic biochemical level, there isn't much room for improvement.  Those genes are highly conserved because they work well just the way they are.

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Dr.GH



Posts: 1957
Joined: May 2002

(Permalink) Posted: Dec. 26 2006,23:32   

I don't really see this thread going very far, but you might enjoy my response to Jonathan Sarfati regarding Imai et al (1999) “Boiled Creationist with a Side of Hexaglycine: Sarfati on Imai et al. (1999)."

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"Science is the horse that pulls the cart of philosophy."

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skeptic



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Joined: May 2006

(Permalink) Posted: Dec. 29 2006,21:21   

Another question, what's are earliest evidence for DNA?  I know we're limited by the nature of the fossil record but what direct evidence do we have right now?

  
Dr.GH



Posts: 1957
Joined: May 2002

(Permalink) Posted: Dec. 30 2006,01:29   

ya see?  I just refuse to try to explain this any more.  OOL demands a solid grasp of geochemistry, and biochemistry.  Plus, you had better do some solid astrochemistry as well.

OOL is far more difficult than the standard creationist crap.  It is much more difficult in the first place, and then you must be ready to deal with the creationist lies and blunders.  I have a 35 page bibliography (and growing) and I have had to limit my attention to areas that I think will be most productive.  

It is just too much!

This is how ID really started.  With Thaxton, C. B., Walter L. Bradley, R. L. Olsen
1984 The Mystery of Life’s Origin.  New York: Philosophical Library.

It was not Johnson, Behe, or Dembski.

Edited by Dr.GH on Dec. 30 2006,01:31

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
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