CONTRADICTIONS IN GENESIS 1-2

It seems as if atheists just can't leave these chapters alone, but continue to try to interpret them according to their own limited perspective. Thus, we were recently treated to some “contradictions” found there by Joseph Sommer, writing in the American Humanist Association web page. But at least he hasn't rehashed the tired objections that (1) six days of creation do not at all fit with the obvious millions of years that it took and (2) the order of creation in Genesis 1 is not the same as the one  determined by science.
A simple but sarcastic rebuttal to those objections is that such people should not be allowed to read books for adults until they have mastered comic books first. But I will go ahead and again address those two issues before proceeding with Sommer's specific objections since such an understanding may help to answer his questions.
The Length of a Day (yom in Hebrew):
Francis Schaeffer states: “The simple fact is that day in Hebrew (just as in English) is used in three separate senses; to mean (1) twenty-four hours, (2) the period of light during the twenty-four hours, and (3) an indeterminate period of time. Therefore, we must leave open the exact length of time indicated by day in Genesis. From the study of the word in Hebrew, it is not clear which way it is to be taken; it could be either way.”  
Getting more specific, the Genesis 1 days are pictured as a typical six-day work week in analogy with mankind's six-day work week. C. John Collins explains in more detail: “The view that I shall advocate can be called the analogical day position: namely, the days are God's workdays, their length is neither specified nor important...” Concerning the refrain, “There was evening and there was morning, the Nth day,” he states that “its effect is to present God as a workman going through his workweek, taking his daily rest (the night between the evening and the morning) and enjoying his Sabbath 'rest.' To speak this way is to speak analogically about God's activity; that is, we understand what he did by analogy with what we do, and in turn, that analogy provides guidance for man in the proper way to carry out his own work and rest. The analogy cautions us against applying strict literalism to the passage.”
Thus, Collins sees the “day” pictured in Genesis 1 as a metaphorically typical Hebrew work day (which  always began in the morning and ended at sundown) rather than the usual Hebrew manner of denoting a standard 24-hour day (measured from sundown to sundown).  As confirmation that this is the correct interpretation, note that each of the daylight workdays in this chapter begins at dawn and ends at sundown.
In addition, we see a clear example of Schaeffer's third meaning for yom in Genesis 2:4 where we are told that God created the earth and heaven “on the day.” Here the first two “days” of Genesis 1 are called “the day,” meaning an indeterminate period of time in this case.
There is actually a second occurrence of yom in Chapter 2, at verse 17 where God warns Adam and Eve of the consequence of eating of the forbidden fruit: “In that day, you shall die.” Of course, they don't die on the same 24-hour day, but begin the dying process from that point of time on. Here again, a broader definition of “day” is in mind.
The Order of Creation
And as to the order of events in Genesis 1, the first thing to note is how close it is to the findings of science compared to the creation myths of any other ancient society that one can name. And that is if one considers it to be presented in a strictly chronological manner, which is not at all necessarily true in this case considering the very poetic way the identical closing phrases read: “And there was evening and there was morning, the Nth day.”
Actually, perhaps the most common scholarly parsing of this chapter, called the Framework Hypothesis, is pictured in Figure 1 below. According to this scheme, realms are first created in a particular order and then populated in the same order. And each of these two parallel sets ends with the same closing chorus (in italics).

                                        Table 1: The Parallel Structure of Genesis 1:1-2:3
Initial Conditions: Chaos (1:1-2)
    Light Created; light and darkness separated (1:3-5)
        Dome of the sky created; waters above and below separated (1:6-8)
            Land and seas created when they are separated from one another (1:9-10)
                Plants are brought forth from the land (1:11-13)
    Lights in the sky separate night and day (1:14-19)
        Birds inhabit the sky, and the water brings forth living creatures (1:20-23)
            Land brings forth living creatures, including man (1:24-28)
                Plants are designated as food for creatures and man (1:29-31)
Final Conditions: Rest (2:1-3)
Sommer's Objections
With that general background, we can now consider two additional “contradictions.” Sommer writes: Chapter 1 reports that the fruit trees were created before the man while chapter 2 indicates they were made after him. Genesis 1:20 says the fowl were created out of the waters; Genesis 2:19 alleges they were formed from the ground.” Let us take these one at a time.
When were the trees created?
As I explained in a much earlier posting, Genesis 2:5-9 looks like a contradiction with the order of creation found in Genesis 1 in that plants seem to come after the creation of man, not before it. This can be explained by looking at a similar construction in Genesis 1:1-2 where an introduction describes what it was like in the beginning – i.e., the earth was without form and void, but the earth doesn't really appear until the third day. In this opening to the Eden story, it similarly describes the situation before the creation: there were no plants on the earth. Then the story zeroes in on the 6th day. 'Erets in verse 5 can mean the whole earth or the land. Probably the latter in this case. This describes the condition of the land in the Middle East in the summer before it rains, not necessarily a time before it had ever rained on earth. Also the garden that God plants in Eden is not necessarily the first time any vegetation appeared on earth.
According to the above scenario, a literary, rather than a strictly chronological, scheme governs the way the material in Genesis 1-2 is presented. First we have a general introduction to the whole process of creation in 1:1-2; followed by a more detailed description of what happens on each day; and finally are told more details concerning what happened on the all-important sixth day.
And there is even a second easy way to resolve this apparent problem. Genesis 2:4b-24 may actually, in the minds of a number of scholars, represent a special creation subsequent to the sixth day of Genesis 1. We can either picture Adam and Eve as the first true examples of homo sapiens on the planet as the culmination of the evolution of man from the hominoids created on Day Six, or they may alternatively be but two examples of homo sapiens chosen from all those on the earth at the time. In either case, it is obvious that the Garden is a specified location in which they are placed and then planted by God with certain edible trees as well as specific animals suited for human cultivation. If either view is correct, we should not at all expect the order of creation to be typical of what had happened on the planet in general during Genesis 1.
Were birds created out of the waters?
This problem question arises in Sommers' mind due to his total misunderstanding of what happened on the fifth day of creation since, as you can see in Figure 1, two realms were created the second day, not just one. Due to the separation of the “waters above and below,” both water and sky came into being. And both are populated on the corresponding fifth day.
Thus, we are told in Genesis 1:20-22 that:
    Let the water bring forth living creatures (whales, fish, etc.)
        Let the birds fly above the earth
    So God created every living creature that inhabits the seas
        and every winged bird after its kind
    Be fruitful and multiply and fill the seas
        and let the birds multiply upon the earth
Note the regular alternation between speaking of the sea and air creatures. Despite Sommers' contention, absolutely nowhere in the passage does it state that the birds were created out of the water. The only way he could have come up with that idea is by sticking to the admittedly faulty King James Version and totally ignoring any more modern rendering which makes the passage more clear. This happens to be a very common ploy of atheists used elsewhere in their writings in attempts to debunk the Scriptures.