I have to wonder why the limit was placed on not discussing origin of the universe.
Because that has jack squat to do with the subject of the thread, which is biological evolution. You want to discuss cosmology? Fine with me. Start another thread. You want to discuss chemical abiogenesis? Fine with me. In another thread.
Limiting the discussion solely to biological evolution is simply a matter of limiting the subject of a single thread to something almost manageable, so that questions in one area don't get lost in replies to questions about another area.
And, contrary to what you imply, the distinction actually made is not an arbitrary one. We know that life exists. How it came about is immaterial to the ToE. We know that the Earth existed well before life arose. How the Earth came to be is immaterial to the question of how life arose (OK, not quite - it can shed some interesting light on the question).
So the distinction is quite well grounded in the different questions posed by those different phases. Not to mention the fact that ToE is primarily biological and biochemical, while chemical abiogenesis is primarily chemical, and cosmology is an astrophysical dicipline. It would be mightily unreasonable to expect the same commenters to cover such a wide range of fields.
Even though some of the older evidence for evolution is questionable at best and dishonest at worst,
Dishonest? Which parts? Questionable-but-not-dishonest? Which parts?
However, no theory of evolution can answer the question of where matter came from.
That being because ToE does not attempt to explain that. ToE explains what happened on this planet after the first life was formed. The formation of said life - much less the formation of the planet - is irrelevant.
To say that atoms somehow organized themselves into complex molecules in violation of the Law of Entropy
Pray tell, what does 2LoT actually say?
[Answer (
http://members.aol.com/darrwin/thermo.htm)])
There is one subtle error in the essay.
I'll leave it as an exercise for the reader to find it.
Next, pray tell, do chemists and biochemists who routinely synthezise complex molecules violate 2LoT in their daily work?
Oh, and while we're on the subject of thermodynamics, what do the other three laws of thermodynamics say?
For a more thorough understanding of how 2LoT (and Newtonian dynamics) work, you could visit the Museum of Unworkable Devices (
http://www.lhup.edu/~dsimanek/museum/unwork.htm#top).
Let's skip forward and postulate matter always existed (a statement of faith, not of science).
First of all, it's not necessary to postulate that matter has 'always' existed. Secondly, the formation of matter is hardly an issue of faith. Astrophysics have the timeline pretty much pat down (although I am personaly in no position to evaluate the soundness of their arguments), and as we speak, investigation into the nature of matter itself is underway at the Centre for European Nuclear Research near Geneva, Switzerland.
How then do we get from atoms to complex molecules
Sorry, you'll need to find both a chemist, and another thread if you want an answer to that question. This link (
http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/PBearth.html) provides part of the answer, but, AFAIK, the whole story has yet to be determined.
to cells
Again, the picture is, AFAIK, incomplete, but RNA has been formed using common chemicals. Lipids - the stuff that makes up our cell membranes - spontaneously forms into closed membranes - that's the trick that makes soap work. And you can probably find more information if you ask a biochemist.
to organisms?
Once you have a living cell, you have an organism. If you mean multicellular organism, part of the story can be found here (
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?db=Books&rid=cell.section.61).
In my entire time as a microbiology major at college, I never found any empirical evidence to support that path.
Argument from personal incredulity.
It just plain violates the Second Law of Thermodynamics.
I reiterate my questions:
Pray tell, what does 2LoT actually say?
Next, pray tell, do chemists and biochemists who routinely synthezise complex molecules violate 2LoT in their daily work?
Oh, and while we're on the subject of thermodynamics, what do the other three laws of thermodynamics say?
It sure makes a compelling argument, though. Are you willing to say that the Law of Entropy applies now, but it did not apply billions of years ago?
I reiterate my questions from above:
Pray tell, what does 2LoT actually say?
Next, pray tell, do chemists and biochemists who routinely synthezise complex molecules violate 2LoT in their daily work?
Oh, and while we're on the subject of thermodynamics, what do the other three laws of thermodynamics say?
Formation of snowflakes does not violate the Second Law of Thermodynamics because they form in an open system
Well, so does life... - or, rather, it forms in a closed, but not isolated system, which is rather more to the point.
and the snowflakes are disordered.
Pray tell, what relevance does 'disorder' have w.r.t. thermodynamics?
They do not conglomerate into snowmen; they remain individual snowflakes.
But they're still just fruitflies. Sorry, cheap shot, but I couldn't resist...
The point here is not that the snowflakes don't form into snowmen. The point is that the snowflakes have lower enthropy than the water vapour from which they are formed. This is compensated for by the fact that during their formation, they have released energy to their surroundings, thus increasing the enthropy of the rest of the world. Which brings us to your reference:
A forming snowflake is an open system. There is mass transfer across the boundary.
More to the point, there's an energy transfer. You can easily design an experimental setup in which the freezing water is a closed system - but it won't freeze unless there's an energy transfer.
If snowflake formation causes a reduction in the entropy of the snowflake, then, by the second law, the entropy change of the surroundings must increase.
That's precisely the point. Now, try to apply this to biological systems.
What about the order of the snowflake? A snowflake indeed appears to have a high degree of order, but remember, we are talking about ordered energy. Ordered energy is energy that is available to do work.
Feh. Now he's confusing enthropy and free energy. A snowflake as a lower enthropy than gaseous water. Inasmuch as enthropy translates to disorder (an analogy, by the way, that is far from perfect), the snowflake could be said to have a higher degree of order. Why the author feels compelled to bring up the free energy of the snowflake is something I fail to understand.
Once a snowflake forms, it doesn't do any work,
Well, technically no bodies do any work. Forces do work. But, contrary to the statement by your source, falling snowflakes do indeed apply forces to their environment, and those forces do indeed do work. Further, if you collect an abundance of snowflakes in a basket, and pour them over a treadmill, you will see that snowflakes can indeed contain free energy...
And, frankly, I fail to see any sense in the rest of the article.
Tree growth and embryonic development do not violate the Second Law of Thermodynamics because the organism expends energy.
You're confusing energy and free energy.
How did random atoms acquire the [free] energy to form molecules, complex molecules, complex organic molecules, cells, tissues, and then organisms?
Same place they do today: Old man Sol. Not to mention the fact that in an anoxic environment, it will be energetically favorable for Hydrogen and Nitrogen - two of the most common compounds in the universe - to form Methane - a compound that contains more free energy than CO2 and water.
And please don't say it was lightning striking a primordial soup in a reducing atmosphere. I did not buy it as a college freshman, and I do not buy it now.
Howsabout volcanic outgassing then?