how did...

This question is far to large to answer here. You could write a dozen books on any one of the questions you pose here. In fact, there have been hundreds of papers and books written on each question you ask. 

It's all about the intermediary steps. For example, you state that: 

"Of course, at the same time the animal's eyes must be fully developed so it can see its food"

Not at all. See: http://www.teachersdomain.org/resource/tdc02.sci.life.evo.nilssoneye/

You can't fall into that "all or nothing" trap. That's a creationist's logical fallacy. 

I suggest "Climbing Mount Improbable" as a good read. It's by Richard Dawkins. It'll start to give you an idea about how the process really worked/works. 

Yeah, the original question is genuinely interesting, but, as Dahan said, it would take far too much text just to give a satisfactory answer to even one of these.

From the second paragraph on, the creationist article starts with misrepresentations (strawmen) and appeals to ignorance, specifically by asking thousands of "how did this, how did that"-questions and posing all kinds of absurdities, obviously with the goal to make evolution seem absurd, but IMO makes the author of the article seem (willfully?) ignorant.

I mean, compare this to the development of a human embryo at conception to a full-grown human. Does the embryo have veins at conception? No. Does it have blood? No. So, according to the reasoning used by the creationist, the development into a normal human is impossible? ...at what point does the embryo's heart start beating?

You can basically replace the word 'animal' with the word 'embryo' in the article, and the article will try to make it seem like birth, the development of new life etc. is completely absurd and impossible.

"Did the embryo develop a partial stomach, then a complete stomach? After the stomach was formed, how did the digestive juices enter the stomach? Where did the hydrochloric acid as part of the digestive juices come from? What about its kidney and bladder? The embryo better not eat anything prior to this."

As a general rule, you must remember that "gradually developing" does not mean "the modern version split into fractions". By this, what I mean is that the organs our bodies contain now are not simply more complete forms of those found in our ancestors'. That would indeed be ludicrous. Take your example of blood spilling out of incomplete veins. Now, the circulatory system is extremely complex, and as both of the replies before mine have said, you are only going to receive a satisfactory answer via thorough research into the subject. However, one thing I can assure you did not happen at any stage was a single part of the body - say, 10% - containing the exact structure we have now, with veins suddenly ending openly somewhere! That would be worse than useless by natural selection standards. I don't pretend to know precisely how any of the systems you described were formed, but there are certainly many books and papers written on each individual subject for those who truly want an answer. For this reason, the "what use is half an eye?" argument is fallacious; half an eye can be very useful, provided you do not fall into the trap of thinking that "half an eye" in an evolutionary sense means one half of a fully-evolved eye. No, "half an eye" could simply mean a collection of light-sensitive cells, perhaps with a lens to cover it. A huge advantage over creatures without any capacity to sense light.

I am glad that you are asking these questions in what seems like an open-minded manner. Your tone indicates - to me, at least - that you are actually looking for answers, instead of asking the questions to make a point. I hope that I am not wrong in this.

Others have answered the intial post quite well, but I thought I'd chime in with a few additional points.

New functions in evolution often appear through a process of excaptation - meaning that some structure that has one function, may happen to be such in shape and form, that it can be taken over into performing a different task. It may initially be quite clumsy at performing that new task, but subsequent mutations and selection gradually hone it for it's new task. Thus, when you look at any modern biological structure - say, the blood clotting cascade that triggers a series of events in us when we get a cut and start bleeding - you cannot assume that the components of the structure always performed the same task in our evolutionary ancestors.

But what happens if a structure is co-opted in this way for a new task? Doesn't the organism suffer the loss of whatever function that structure used to perform? Not necessarily - there are at least two ways in which this can happen without any harm to the organism. First - perhaps the environment has changed so that the old function is no longer needed, and thus losing it is of no consequence. Second, and more commonly, in the process of copying, a stretch of DNA is accidentally copied twise - so that the new cell ends up with two copies of the same stretch - this stretch may contain one or more genes.

If this new mutant cell happens to be a germline cell - a cell that ends up as a sperm or an egg cell, then this mutation can be carried to the offspring, so that the offspring now have this extra structure in the DNA of all their cells.

Now you have two copies of the same gene, and thus if one of those genes gets excapted to a new purpose, the other copy of the gene still carries on the old function.

Indeed, the blood clotting cascade we humans (and other mammals) have, is composed of a sequence of genes which are slightly modified versions of the same gene, brought about by just such duplication and subsequent modification of the genes. Even the original gene that was duplicated to start this blood clotting cascade has been identified - if I remember correctly, it's a gene involved in digestion.

But how could an animal survive BEFORE the blood clotting cascade evolved through this process of excaption, duplications and modifications? Here we must point out that there are still organisms around, living quite happily without such a cascade - how can they manage? The answer is that organisms without efficient blood clotting, don't have (nor do they need) high blood pressure - their blood flows slowly, and a cut isn't as dangerous as it would be for a mammal without a good clotting system. The components of blood other than the blood clotting products are also somewhat sticky, though not as sticky as the specialized blood clotting products, and this is sufficient to clot a wound if you have really low blood pressure.

The blood clotting cascade evolved alongside a cardiovascular system that utilized an efficient pump and high blood pressure, and this happened gradually - with every improvement in blood clotting giving opportunity for higher blood pressure, and every increase in blood pressure giving a selective advantage to any improvement in blood clotting.

So the answer to that flood of questions is briefly that:

1) The systems of the body didn't necessarily initially serve the same purpose that they do in modern organisms.

2) What is essential for a modern organism may not have been essential for it's ancestor, due to other differences throughout the body.

3) Gene duplication, excaption and gradual modification provide the fuel for selection to work on, to produce new structures, and these effects work throughout the body, on all systems in parallel, so that no organ evolves alone, detatched from the rest of the systems, with the other systems in modern form "waiting" for, say the liver to finally evolve. Thus there are no "half formed" animals anywhere among our evolutionary ancestors.

As others have mentioned, numerous papers and even whole books have been written on specific answers to the specific questions, and those are available for anyone with the patience and interest to learn the necessary, and often quite difficult, biology involved, but I hope the answer I've given, and the example of blood clotting has shown you the general shape of the answers, and why those questions aren't in any way "stumpers" for evolutionary biologists, but rather reflect a lack of understanding of the nature of evolutionary processes on the part of the person asking. But that is ok, as, if the questions are made honestly and not as rhetorical attacks, that understanding is out there to be gained for any curious mind.

Alphastar18 wrote:  'I mean, compare this to the development of a human embryo at conception to a full-grown human. Does the embryo have veins at conception? No. Does it have blood? No. So, according to the reasoning used by the creationist, the development into a normal human is impossible? ...at what point does the embryo's heart start beating?'You can basically replace the word 'animal' with the word 'embryo' in the article, and the article will try to make it seem like birth, the development of new life etc. is completely absurd and impossible. Did the embryo develop a partial stomach, then a complete stomach? After the stomach was formed, how did the digestive juices enter the stomach? Where did the hydrochloric acid as part of the digestive juices come from? What about its kidney and bladder? The embryo better not eat anything prior to this.'

I disagree that the development of an embryo is a good analogy to neo-Darwin biological evolution.  Development of the embryo is not driven by a random process.  It is driven by a precise, non-random process as DNA in the embro turn developmental genes on and off in a specific and timed order.  The reason half formed organs do not fail, is because the organs are not expected to be used until construction is complete.  Development of an embryo is analogous to a very complex computer program executing.  In fact, it is the most complex molecule in the universe and is the most complex program ever discovered/designed (if you will allow me to use the word 'design'-a precise synonym does not come to mind).  In contrast, neo-Darwin biological evolution theorizes that a random process of errors in this DNA program causes new, useful information that eventually forms new bio-chemical pathways, tissues, and organs or changes the way in which present pathways, tissues and organs function.  Theoretically this random process of duplication and mutations in the duplicated sections of DNA resolve survival issues of the creature population at a faster overall rate than the problems caused by genetic diseases cause creature deaths. 

Thank you for this open forum on the topic and for allowing me to express my opinion that I disagree embryo development is analogous to neo-Darwin biological evolution.

I don't really understand your point here - if a mutation provides more detriment than advantage to the survival of the organism carrying it, that mutation will tend to be weeded out by natural selection - the very NON-random process that guides evolution. This same selection will ensure that mutations that provide a survival advantage will tend to spread in the population. The process works quite regardless of the ratio of harmful mutations to beneficial ones; only the speed of evolutionary change is affected by such considerations. There's nothing speculative about whether it happens - it is the unavoidable logical consequence of natural selection acting on variation.  If I'm missing the point you tried to make here, please clarify what you mean by the statement quoted above.

Another less important comment:

While you do have a point as to the strict applicability of the embryo analogy, your point that in embryology the organs that develop are not needed prior to their completion, thus allowing half-formed organs in the process, also applies to the evolution of those organs - their current function was not needed (or needed to the same degree) in the organisms in which the organs in question first arose.

For an example, see my earlier post above on the evolution of blood clotting - the process of evolving a "necessary" organ begins in an organism for which that organ is not necessary, but some functionality that such an organ might confer would be advantageous. Thus, any changes towards the initial stages of such an organ are favored by natural selection. Once the earliest rudimentary functions of the organ are crudely functining, further changes on the organism can then exploit the existence of that rudimentary organ, causing the body to evolve a dependence on that new function - with that dependence, a selection pressure is given to further enhancements of this new organ and it's function, which, in turn, allows further modifications of the body that would not have been possible without that organ.

Thus eventually you end up with an animal with complex organs without whose complex function the animal could not survive. However, as should be clear from the logic of the explanation above, that was not the case for the ancestors of that animal.

In this sense, the analogy does work - the modern function of modern organs was not needed in the earlier evolutionary stages of that organ, due to the different needs of the bodies that carried the organ.

Of course, in the case of the developing embryo, it is nourished and sustained by the mother's body, for which there is no analogy in the evolutionary process. That's the trouble with analogies - they rarely provide a 100% match.

Embryology is also, as you say, guided by genetic instructions - however, evolution is ALSO an algorithmic process - replication with random variation, and non-random selection applied to each generation, favoring some changes over others, repeated generation after generation, is no less a "program" than the one more explicitly coded in genes. The only difference really is that the genetic program's outcome is predetermined by the genetic sequence, while the outcome of evolution is open-ended - it is a guided process, like embryology, but guided only by the environmental pressures applied to each generation, rather than a rigidly set code.

Another thing absent in the analogy is the guidance of a running program.  There is no DNA program running to turn the need for half functioning organs on or off.  The reason the baby gets nourishment from the mother is that it is not attempting to start it's own self-contained nourishment processes until they are completely constructed and the reason for that the processes are turned off or powered down. The genetic development program is very specifically keeping them turned off until they are ready for use.  It is one of the most directed processes observed.  This is not analogous to a completely random process of adding errors to the DNA program from which a quality control process (natural selection) weeds out the most fatal and allows the theoretically benefical errors to propogate.  Quality control processes such as natural selection tend to maintain status quo and not practice research and development.  Again, thank you for your patience and allowing me to contribute in this open forum. 

 Again, I refer you to my first post in this thread, where I explain, as an example, the method by which natural selection, acting on variation builds both the need for a complex feature AND the feature itself concurrently, so that you never have a need for a function before it comes to be, but once the feature is there, the organism may become dependent on it.

Again, blood clotting is a good example - if you don't have a circulatory system that relies on blood being pumped throught the body at high pressure, you don't need a very efficient and specialized blood clotting system. But any beginings of such a system, would confer the organism an advantage over others in it's population, others, who relie on (the still sufficient) non-specific stickiness of their blood to handle cuts and ruptures.

Once this slight advantage is conferred though, this allows any mutation that would slightly increase blood pressure to be beneficial, in any organism that carries this earlier mutation! (In individuals without that earlier mutation, higher blood pressure would make any bleeds very hazardous.)

Increased blood pressure, in turn, allows for larger body size, and more energetic activity - and thus the initial mutation not only confers the immediate advantage of a better system of clotting, but opens up avenues for new mutations, which would previously have been detrimental, to be beneficial!

If you give this a little thought, you'll see how this method will produce bodies with complex interdependent systems.

In other words, there is no NEED for a genetic program to switch "needs" on and off in a pre-arranged manner - the fact that the need and the function co-evolve graduall is guaranteed by the algorithmic process of random variation on which natural selection acts.

You say: "...a completely random process of adding errors to the DNA program from which a quality control process (natural selection) weeds out the most fatal and allows the theoretically benefical errors to propogate."

There is nothing "theoretical" about beneficial mutations - the are numerous observed  and well documented instances of a mutation confering a benefit, which natural selection favors!

There's even a beautiful study in which the development of a two-part system (a system which needs both parts to confer the advantage) evolved under laboratory conditions under the scrutiny of researchers, through two separate mutations. The details of this study are absolutely fascinating, as the researchers had remarkable foresight and ingenuity in their methodology, which allows for the consistent repetition of the experiment with the same results. (If you are interested, I'll be happy to give more detail.)

Further, natural selection not only weeds out "the most fatal" mutations, but has been shown to act on remarkably slight differences, both through mathematical models, and field studies of cases in nature, as well as laboratory experiments.

You say: "Quality control processes such as natural selection tend to maintain status quo and not practice research and development." 

This is entirely untrue, as is demonstrated by both laboratory experiment and field study - natural selection certainly does not maintain status quo, how could it? If you understand the mechanism, how could it NOT result in constant change? What mechanism would prevent change?

"Research and development" is precisely what mutation + natural selection amounts to - it is such a powerful mechanism for finding new solutions that it has even been utilized in computer programming, in evolutionary algorithms, to build novel solutions to complex problems.

The evolutionary process is essentially a blind "trial and error" process - make random changes, preseve the ones that work, discard the ones that don't. Mare random changes to the preserved, and again keep those that work, discard those that don't. Rinse and repeat. The result of this process isn't the maintenance of status quo, but constant change that opportunistically builds new structures.

That is the very beauty of natural selection - it is such a simple mechanism, yet it yields endless variation and functional complexity.

"Again, thank you for your patience and allowing me to contribute in this open forum. "

You are quite wellcome.

thank you for your patient replies.

Yes, I suppose my analogy is flawed in that way, but I still think the creationist article tries to use false reductio ad absurdums.