Monday, January 24, 2022

Why The Retrovirus Argument for Evolution is No Threat to the Christ-Centered Model

What is the strongest evidence for evolution? I had a dialogue recently where someone put it like this....

We have pseudo genes for many olfactory receptors that our distant cousins supposedly have? Or how about the fact that we share the same endogenous retroviruses as the great apes in the same place in our genome? That's pretty powerful to me.

The term for the trail of such genetic clues is "Nested Hierarchies". There are some genetic snippets that we share only with chimpanzees. A wider set is shared with chimpanzees and gorillas. This pattern is hard to explain in terms of de novo special creation as most people conceive it. While Winston Ewert has done some interesting work regarding other explanations for these nested hierarchies, I'd say my acquaintance is correct. The nested hierarchy evidence strongly supports common descent.  

However, the evidence isn't quite the slam dunk that many naturalists believe. The question is in the nature of the descent. Proving the claims of naturalism is very difficult. Much more than most of its adherents let on or even understand. If they insist that nature alone explains all there is, no exceptions, that is quite an expansive claim. 

Now I said that the retrovirus data was hard for creationists to explain, but much depends on your definition of "de novo" creation, and your definition of "evolution". Despite all of the internet flame wars, there are some commonly accepted definitions of evolution which would not exclude creationism and vice-versa. Naturalism is excluded by creationism. But creationism is not excluded under some definitions of evolution. Many definitions don't have naturalistic premises built into the them, even if readers often impose them from the outside.  

For example, if God wanted to go from a fish to an amphibian I suppose he could have started from scratch. But He also could have done what I did as a coder and cut and paste from my old work and then just tie it together with more modules so that it is a new program. He could have gone from amphibian to fish in one move, but He did so by starting with lungfish "code" which He then modified as needed. 

When I re-purposed old code into a new program, on the first step I pasted in a big block. I would even leave in some unused code. or code that no longer does anything. This is a fair parallel for some of these genetic bits we see. They are analogous to unused "code". Suppose God did something like this when He was forming new kinds. Notice how if this happened often enough, the result would still look like the nested hierarchies that we see. This even though God intervened personally a million times. This would be a form of special creation that might also meet some definitions of evolution. For example it would be "Change in gene frequencies over time" but the source of the biggest changes would not be from nature acting alone. This scenario is definitely creationist, but under some definitions it is technically also evolution. It is naturalism which is excluded. 

Normally it is considered bad programming form to leave in any dead ends or extra code that you don't use for the new program. So some might be tempted to rule my scenario out on the grounds that "God would not be a worse coder than we humans". But this is short sighted. The big reason we clean up code is because it will confuse us or other programmers who look at it later if there is a bunch of code that is no longer called on left laying around. We do it because we are not sharp enough to see right away that it isn't functional or essential. That limitation doesn't apply to God. He doesn't need to clean up after Himself so He won't get confused later. 

Do you think it is unfair for me to describe such a scenario because it would be so hard to tell from naturalistic evolution? Well, I am about to take it further and if it is unfair it isn't my doing. Like I said, naturalists have set a high bar for themselves with the expansiveness of their claims. If they want to make absolutist all-encompassing claims then they should have to provide evidence of the same nature. As you will see, they don't have it and I don't expect they will be able to obtain it. It is beyond the scope of this post, but I'd make the case that not only is the assumption of naturalism as a philosophy unjustified, they can barely hang onto the idea that it is reasonable to think that known natural processes could have produced some of the biggest changes we see in earth's biota. 

Taking my scenario above farther, and extending a bit of an olive branch to all but the more ardent naturalists, there is another explanation that I think blends creation and evolution together in an almost 50/50 manner.......

Suppose instead of going from fish to amphibian by cutting and pasting code and building a new creature, God simply adapted a particular school of fish much like our genetic engineers do. Maybe He did it over a few dozen generations instead of building a new creature all at once. But all of the changes He did were acts of creation, not something that nature did or was likely to do in the time allowed. He just did it starting with a population of fish rather than taking some fish "code" and modifying it to make an amphibian "de novo". Rather He made "de novo" changes in existing organisms until He wound up with a "de novo" organism. Fifty generations later you wind up with amphibians that would still have the genetic markers in question. Is that "evolution"? Yes, under some definitions. But it is also creationism because God repeatedly intervened in nature to enable new forms of animal life. It just isn't naturalism.

This might be where some naturalist would object that whatever god operated like this, it would not be the one in scripture. That's because there is a class of unbeliever who thinks that Christians should not be able to alter the interpretation of scripture that was predominant when they were born, but they, the naturalists, should be free to alter their interpretation of evidence from the natural universe on a regular basis. I am not a big fan of gross hypocrisy, so I don't indulge such double-standards. 

Creationism isn't limited to God forming creatures directly out of earth. Although I do believe that happened within the garden, that's not what the text says happened in the larger world outside. In the Christ-centered model chapter two isn't a retelling of the same story as chapter one. It is a tale within that larger tale, of the initiation of God's plan to reconcile that larger creation to Himself, ultimately through Messiah. Yes the limited set of animals in the garden were specially created, but they were created as domestically useful versions of some of the animals outside the garden

What about the animals made outside the garden? The text gives us less details about the larger work of filling the world with the much larger variety of animals there. All it says is that God commanded the earth and seas to bring them forth.....as if creation itself had some creative power...but then says that God involved Himself in this process. That sounds a lot more like what I have described above. So if an unbeliever wants to undermine the veracity of the text, the above scenarios are the kinds of things they would need to discredit. I don't think they can. They are more likely to discredit themselves trying. 

I would add that even an act of de novo creation like the kind described in the garden, if it was based on an existing type, could still be expected to have all those markers. For example, I think the more limited set of creatures God formed in chapter two were based on more domestic strains of the ones made in chapter one. If He formed some cattle that were suitable for domestication with an Auroch gene template, then they would have the same genetic retrovirus profile as their wild brethren. Why bother to take it out? It is what He was adding or changing functionally that was what was important. And those wild ones He could have formed step by step from a stem mammal in the gradual manner I described for fish to amphibians above.

With man, the situation is different. God wasn't assisting the earth or seas with a command He gave. He did the job Himself. In the case of Adam, by direct formation from earth elements. I believe that scripture teaches there were already people, humans like us, outside the garden when Adam was formed. Whether they were formed in the same way as Adam or not is an open question I guess, but it was God's doing and not nature's. But once again, why start from scratch if you have some perfectly good hominin code available? 

When most "theistic evolutionists" talk about this I think they are not saying what I am saying. They would be more like DIESTIC evolutionists. Where God set up all the dominos in advance so that when He knocked the first one over He could just sit back and watch the rest of them fall.

That isn't what I am talking about. The universe can't do God's will without God's help (thus it is a fit universe for creatures like us). Even if He told the SEAS to bring forth living creatures, they can't do it without Him. Maybe they could try for 100 million years and get stuck at the Ediacarans. When He steps in we get the Cambrian. 

Those with faith in naturalism may ask "why is assisting nature even necessary" because they are convinced that nature alone could do the job within the time frame she had. But the truth is we only know what has been done. We don't know if it was nature alone doing it. Indeed Gunter Bechly's three biggest objections to nature alone being responsible still stand. These are the information problem, the search space problem, and the waiting time problem. The scenario I described above, pulled straight from my view of early Genesis, would solve those problems even if it isn't a natural solution. 

The Christ Centered Model has no problem with any of the endogenous retrovirus evidence, or any other evidence from either history or the natural universe. It only takes issue with the a priori insistence that nature alone produced everything we see. The evidence itself is all reconciled in the most amazing manner- assume the text is speaking of the work and person of Christ from the start. If you do that first, what you get effortlessly reconciles all the evidence from nature and history to the text. 



Saturday, January 22, 2022

Why Mark 10:6 and Matthew 19 Don't Point to a Young Earth

  Mark chapter ten and Matthew chapter nine contain two accounts of the same event. The Pharisees are questioning Jesus about marriage and divorce. Young Earth Creationists have appropriated these verses to claim support for the belief that Jesus taught that the earth was young. I did address this somewhat in my book, but it keeps coming up again and again so I want to address it here as a stand-alone topic. 

First, let's look at the two passages in context. For Mark 10:2-9...

And the Pharisees came to him, and asked him, Is it lawful for a man to put away his wife? tempting him.  And he answered and said unto them, What did Moses command you? And they said, Moses suffered to write a bill of divorcement, and to put her away. Jesus answered and said unto them, For the hardness of your heart he wrote you this precept. But from the beginning of the creation God made them male and female. For this cause shall a man leave his father and mother, and cleave to his wife; And they twain shall be one flesh: so then they are no more twain, but one flesh. What therefore God hath joined together, let not man put asunder.

They reason that since Jesus said this joining together of Adam and Eve as man and wife was from "the beginning of the creation" then this implies that there could not be millions or billions of years between the creation of the universe and the ordination of marriage. 

Matthew 19 has very similar wording.  

3The Pharisees also came unto him, tempting him, and saying unto him, Is it lawful for a man to put away his wife for every cause? 4And he answered and said unto them, Have ye not read, that he which made them at the beginning made them male and female, 5And said, For this cause shall a man leave father and mother, and shall cleave to his wife: and they twain shall be one flesh? 6Wherefore they are no more twain, but one flesh. What therefore God hath joined together, let not man put asunder. 7They say unto him, Why did Moses then command to give a writing of divorcement, and to put her away? 8He saith unto them, Moses because of the hardness of your hearts suffered you to put away your wives: but from the beginning it was not so.

Matthew nineteen also uses the phrase "the beginning" but does not specify the beginning of what. Mark includes the phrase "from the beginning of the creation" and so this is the passage most used to support their argument that "the beginning" Jesus was referencing was the beginning of the universe.

Here is an interlinear of the key verse Mark 10:6...note the word translated "creation"

Notice that the Greek word translated "creation" here is ktiseos. It does not mean "the universe" or "the world". That would be some form of the Greek word "kosmos". Rather, ktiseos means "the created thing" or the act of creation if used as an adjective. 

If the Holy Spirit had wanted this conversation to contain evidence of a young earth, Luke could have been inspired to write "kosmos" there and put the thing to rest. This did not happen and the word used does not mean "the universe" or "the world" in this context, though as we shall see it can mean that when the appropriate modifiers are present. I don't even think it means humanity per se, because the created thing that is the topic of this passage is the institution of marriage. For most, that distinction is without a difference because Eve was created to be the wife of Adam and that all happened as one interconnected act. But if there were men and women outside the garden before that act, it would not necessarily be speaking of them. It would be speaking of when God ordained the institution of marriage that is the topic of the conversation in this passage. See the definition of the root word here, ktisis...

So it's meaning is very much in tune with applying to the establishment of an institution such as a the political union of people in a city or their personal union in marriage. It is basically "the created thing(s)", so it is sometimes translated "creature". Can this mean the world or the universe? Yes. When the text shows that the world is the "created thing" it is referring to, then it means the world. If "all things" are the created things it is referring to, then it means the universe and beyond. Here are some examples where a form of ktisis can legitimately mean the world or all things...
“For since the creation (κτίσεως) of the world (the "created thing" is specified by "of the world’)… [God’s invisible attributes were] being understood by what has been made…. - Romans 1:20 

“For the eagerly awaiting creation (κτίσεως) (the KV translates this "the creature" until verse 22 where it says "the whole creation" and this is more correct. This verse and the next don't specify what created thing it is referencing until verse 22 where the ambiguity is resolved when it says "all" that was created.) waits for the revealing of the sons and daughters of God.”- Romans 8:19

“He is the image of the invisible God, the firstborn of all creation (κτίσεως) (here again the word is modified by saying "all". "the created thing(s)" What created thing? Answer: All.): for by Him all things were created, both in the heavens and on earth… all things have been created through Him and for Him.” -Colossians 1:15-16 

“...mockers will come with their mocking, following after their own lusts, and saying, ‘Where is the promise of His coming? For, ever since the fathers fell asleep, all things (‘all things’ specifies that the created thing referenced is "everything") continue just as they were from the beginning of creation (κτίσεως).’” - 2 Peter 3:3-4

“...the world has been created (κατηρτίσθαι) by the word of God so that what is seen has not been made out of things that are visible.” (Here it specifies what the created thing is, the world.) - Hebrews 11:3

So I hope you can see from these examples that this passage isn't evidence that Jesus was speaking of a young earth. There is no just basis to shoehorn that meaning into Jesus teaching the Pharisees about marriage and divorce. Jesus was telling them that since the beginning of the creation of marriage itself, God had meant for it to be a joining of male and female. And since it was God's doing, man should not undo it. 

It isn't even necessarily taking about the beginning of the human race, except that the existence of male and female humans is a precondition for the two being made one flesh. The act of the formation of Eve from Adam as a template for us establishes this union and thus it is tied into the formation of Adam and Eve. So if Adam and Eve are the only humans then it is a distinction without a difference, but in principle if there were other humans outside the garden before this then the "created thing", the ktisis, that Christ is referring to here is the institution of marriage, not even the formation of humanity in general.

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Friday, January 21, 2022

Deconstructing Jeanson's Study on Y-Chromosome Recent Common Ancestor

 Dr. Nathaniel Jeanson has released a study on Y-chromosome mutation rates and its implication for the age of Most Recent Common Ancestor (MRCA) that has caused quite a stir. This is because the results of his study point to all or almost all living males descending from a single male ancestor (or at least a small group of closely related males) as recently as 4,500 years ago. 

Not coincidentally, this roughly matches the date of the flood of Noah if one applies the reasoning of Bishop Ussher to the dates of the Masoretic text of Genesis. Ussher's reasoning is missing something, and there is a case to be made for the Septuagint numbers matching the original autographs, but even if you double, triple, or multiply this number times ten, the implications of what Jeanson is claiming are still astounding. His findings fly in the face of a lot of other scientific research. That in itself is a red flag, though not necessarily disqualifying because much advancement in science has come from showing that what the previous group of scientists believed was either mistaken or incomplete in an important aspect. 

Nevertheless, Jeanson has this one wrong, and I am going to explain why. Real science should not just dismiss contrary findings, but also be able to explain why they are mistaken. Sadly, I haven't found any unbelieving science aficionados either willing or able to do this. Thus it falls to me, a creationist (albeit one who thinks creationism and evolution have a complicated relationship) to explain to unbelieving skeptics and believers alike as to where Jeanson went wrong. He is most wrong, but that doesn't mean I think the current mainstream date is correct either. The latest research shows that conventional wisdom also has the Y-haplogroup MRCA date wrong. Taking this latest information into account I explain here why I think it is very possible that the 'real' Y-haplogroup MRCA date is only between 50-70 thousand years ago. 

To the unbelievers, if you read through this and decide that my science and reasoning are sound, well I tell you that my theology is way better. It is more worth listening to than what I say about science. And I ask you to consider it with an open mind and dare to sincerely ask God to show you Himself in it. 

To the believers I say, do not be dismayed if the earth and humanity are older than you thought. Nor even if you are mistaken concerning what the flood was about. As Christians, our hope isn't in never being mistaken, but that Christ has atoned for all of our sins, and loves us through our mistakes. Believe me, the text can still be true, and is true and is more wonderful and points more to the truth of Christ than you (or I ten years ago) could have even imagined. The church has been misreading it, but that doesn't make it false. It makes what they have been saying about it false. In former times, these errors did not matter, but now in order to witness the truth of God's Word we must cast aside what we thought it said before and be like the more noble Bereans who study carefully. When we do, we will find that the narrative of the text is Christ-centric and that just seeing it that way resolves all of these supposed conflicts with science. 

Now before we start I should point out the nature of MRCA data. It is theoretical, it may not even be describing an event that really happened. For example, if humanity started as a population instead of as a single couple, as most skeptics and I (though I still believe in a literal historical Adam) think, then the "MRCA" number may be "how far in the past something that never happened occurred". You can't say humanity is over 200,000 years old just because the MRCA date for Y-haplogroups or anything else is that far back. The date would only apply if humanity sprang from a single couple and did not start as a population. If they started as a population with some diversity then the MRCA date is going to be much older than the actual date of our species. I don't want to go into the weeds here, so go to what I write about that here for more details if you care to. 

Even in this study, were it correct, can't tell us that all male humans spring from a single common ancestor only 4,500 years ago. It could be that there were a thousand fathers at that time and they all had the same Y-haplogroup with little genetic variation on this chromosome. Or it could be that half of them had other Y-haplogroups but they failed to leave any male descendants in living populations. We know for example that Y-haplogroup diversity declined precipitously from 9,000 to 5,000 years ago before making a rebound (which I fold into my theology here). The recent decline in Y-haplogroup diversity is real, but that doesn't mean that humanity was ever reduced to a single male. 

That said, I am now going to explain where Jeanson went wrong. I need not delve into the technical jargon and minute details of his methodology to do so. His mistake is so fundamental I don't have to do much of that. I say "mistake" but I think there is more than one in his paper, but these would be smaller errors that he used to massage the data more closely to his desired outcome once he got things in the same ballpark. I am going to describe how he got them in the same ballpark when they should not be. 

He starts off with a long discussion of the low-coverage scans of Y-haplogroup data which defined previous such studies. He points out that these miss a lot of variations/mutations. He is right about that and also right about the way time-depth has been calculated. We take the known mutation rate from the short term, such as father to son, and then compare it to the total differences we have found among the various types of Y-haplogroups. If we find 10,000 more mutations amongst all haplogroups as we find between father and son (on average), then we conclude that there were 10,000 generations needed to produce the mutations that we see. If we assume a reasonable generation time of 20 years, then the MRCA was 200,000 years ago. That is the basics. The fine-tuning gets more complicated of course, for example factoring in back-mutations which can mask the total number of mutations that have occurred, but we need not go into those details. 

Notice that when you do the procedure I described above, finding more mutations between father and son (compared to total human mutations), the shorter the time to the supposed MRCA. Conversely, the more total mutations there are in all humans (compared to the number of mutations in father-son) then the further back in time it would be to this MRCA. So the trick, if one is attempting trickery and I am not saying for certain that Jeanson is, would be to measure father-son mutations in a way which would find as many of them as possible, but measure overall human Y-haplogroup diversity in a way which would leave many of the mutations and variation unfound. For a recent date, you want to find lots of mutations in your father-son searches but less in your all-of-humanity searches. Jeanson has found a way to do this discretely.

You can see this when you consider the effects of how well your data collection method picks up these mutations. If you have a low-coverage scan, it may only pick up a fraction of the mutations/variation that are there. Let's say one out of four for the sake of discussion. How can you then get a good number? Through the miracle of averaging. So long as the same collection method is used for determining both father-son rate and total amount of diversity in humanity, the numbers derived should still be sound. Yes, you missed 75% of the mutations in humanity (not in number of Y-haplogroups but all the differences in them) but you also missed 75% of the variation between father-son. Because of that, your time to MRCA should be just as sound as if you found all of the variation in both sets you are comparing. 

Remember I started by saying Jeanson spent time discussing low vs. high coverage scans? His father-son mutation rates are derived from high-coverage data. He uses that to develop what he calls "tips" which are in effect tiny branch lengths. He then compares that to branch lengths of all Y-haplogroups derived from other studies BUT, those studies used low coverage scanning of the genome. So his data for the father son rate was obtained via a method that maximized the number of mutations found, and he in effect compared that to total branch lengths for humanity obtained via a method that undercounted these mutations. 

I taught middle school science, almost all in public schools, for thirteen years. I taught them that for the results of an experiment to be valid you have to collect the data you are comparing under the same conditions. You can't find out who is the best free-throw shooter by having one person go outside on a windy day and shoot with a lumpy ball in dress shoes at a court by the highway with a bent rim and no net while the other person uses their favorite ball in a quiet gym. 

To stick with our example, if high-coverage data found four times the mutations of low-coverage data then the father-son data might find 10 mutations instead of 2.5. The total number of mutations for mankind was derived from low-coverage methods that perhaps found 25,000 mutations when high-coverage methods would have found 100,000. The real numbers would be different but the proportions are what is important here. 

So using high-coverage data on both ends might give us:

100,000 total mutations / 10 father-son mutations   = 10,000 generations. If generation time is 20 years that is a MRCA date of 200,000 years ago.

Or using the low-coverage data on both ends might give us:

25,000 total mutations / 2.5 father-son mutations  = 10,000 generations. If generation time is 20 years that is a MRCA date of 200,000 years ago. 

But what Jeasnson did, once you follow the shells, was use the higher rate for the father-son side and the lower rate for the all of humanity side.....

25,000 total mutations / 10 father-son mutations  = 2,500 generations. If generation time is 20 years then that is a MRCA date of 50,000 years ago. 

So that takes care of 145,500 of the 195,500 years Jeanson needs to lose. Now he just needs to whittle off another 41,500 years and he has a MRCA date consistent with his (almost certainly incorrect) date of the flood of Noah. Bear in mind if the high-coverage scans pick up even more mutations relative to the low-coverage scans this reduces the dates down even more. 

An example of how he whittled the dates down further in an invalid way? I think he did this in part by assuming a generation time of not twenty years, but fifty years (see his supp. table nine). That is, he figured the average age of the father at the birth of the average son was fifty. At first you might think this would make his problem worse because it would be multiplying by longer generations, but this is where his "filtering" came in. What I think he did here was say "we are looking at this data with ten father son mutations when the average age of the father is twenty, but evidence indicates fathers at fifty have a lot more mutations so we need to adjust the father-son mutation rate up for that". It looks like from supp, figure nine that he adjusted the mutations up four times or even five times. This is masked because he used generation times of 15 years and fifty years. 

In other words one that is unreasonably young for average age of father and one that is unreasonably old. If you consider a more reasonable age of twenty for age of father, his use of age fifty is jacking the generation time up 2.5 times (50 vs. 20) but his mutation rate goes up four times or even five times.  Let's say it is only four and do the math again.

25,000 total mutations / 40 father - son mutations = 625 generations x 50 years per generation = 31,500 years. 

He's managed to lose another big chunk of time. Again, these are just example numbers except for those from his "supplement nine". To find his exact numbers and use them would be very tedious, but in principle what he is doing is going to drive the numbers way down. Once we see this, the details of his actual calculations are not important. 

The above doesn't even consider something I mentioned earlier- back-mutations. A back-mutation is when a gene mutates, and then mutates again to its previous state. If you take a snap-shot at the end, you might think no mutations have occurred when in fact two have. If humanity is as young as he thinks, this would not be a huge factor because the number of back-mutations would not be huge, but it would not be zero either. If mankind has a long history stretching tens of thousands, or even hundreds of thousands, of years in the past then it is a bigger factor and one which would raise the number you use for "total number of mutations in humanity". In other words, this would push the MRCA date back in time. Jeanson doesn't account for it. 

But let's just focus on the different scan-coverage rates. It makes a huge difference that gets rid of almost all the years Jeanson needs to lose to support his conclusion. From there he could make much smaller mistakes, or to look at it in a more sinister light, find smaller ways to massage the data, to whittle off the remaining years he needs to lose. I have some idea about other places he did the smaller data massages, but there is no need to explore them. The methodology is already wrecked. 

I conclude that this paper is fundamentally flawed. But I also conclude that Jesus Christ is God and that the scriptures are, when properly understood, true. YEC are wrong about early Genesis, but they are not wrong about Jesus, and they are not wrong about the scriptures being sacred. 

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Friday, January 7, 2022

Digging Deeper on Genesis 1:5 and the Nature of the Days


Is there a conflict in Genesis 1:5? 
Genesis 1:5 KJV — . And God called the light Day, and the darkness he called Night. And the evening and the morning were the first day.

If God called the darkness night, and He called "the LIGHT" day, then how can the night be anything but the condition which precedes the day rather than a part of the day itself?

This of course must be juxtaposed against the last phrase " the evening and the morning were the first day". The first part says that the LIGHT is day and the darkness is something else. The last part says that the evening and the morning together were the day, implying that the darkness WAS a part of the day. So a literal reading of this translation of the text is contradictory.

So there are three options. 1) Accept that the text immediately contradicts itself 2) pick one phrase as what you believe and pretend the other does not say what it says or 3) go to the Hebrew and see if this isn't a translation issue and the Hebrew itself is consistent.

An obstacle with option 3 - the interlinear tool on BLUELETTER BIBLE is flawed. Particularly with the last phrase of the verse. Look at the interlinear of the last part of the verse on BLUELETTER. It translates "haya" as "and" twice, but if you click on the number for the word, h1961, you will see that isn't what that word means. It means some form of "was" or "were" or "there was". It just has the character for "and" in front so that it should not say "and evening and morning" but "and there was evening, and there was morning". The BLUELETTER is just taking the first character that modifies the "was" and ignores the "was"

They also end the verse with the claim that the last three words are "yom- ehad - yom" and incredibly translate the first "yom" as "the". The - first - day. So it has the wrong words and the wrong meaning for those words. This isn't the way this verse ends in other interlinears and "yom" does NOT men "the". So Blue Letter Bible's interlinear is flawed and it doesn't take much looking to see that it is flawed. You will see this is a consistent pattern. When there is a root word that is modified to have a "the" or "and" in front of it, they ignore the root word and just list the meaning of the implied modifier. 

In contrast, here is biblehub's interlinear of the verse. Here you can see that the proper translation of this phrase is "and there was evening, and there was morning- day one". Further by clicking on the small blue "parts of speech" notes beneath them, you will see that these verbs are "consecutive imperfect". So it is referring to a series of events one after the other. Evening, then morning. It isn't co-joining the two as it would if the evening and the morning were both part of the day, it is saying that two events happened consecutively. 

Once you see it, the apparent conflict between the LIGHT being the day as opposed to the dark being something else, and the last part of the verse implying both darkness and light are the day- is resolved. The morning is the start of the day. The evening is what precedes the day, it isn't a part of it.

"and there was evening, and there was morning- X day".

That is saying something different than "the evening and the morning were the X day". With the KJV translation, there is a conflict because it seems the night is part of the day. With the former translation there is no conflict with the rest of the verse because it could just as easily be saying that the morning was the dawn of the new day and the evening was what was before the day, and not part of the day itself.

Many translations of scripture now recognize that the phrasing of the last sentence of Genesis 1:5, repeated throughout the chapter, is more ambiguous regarding this issue. The ESV is the main bible used where I attend, and it says "there was evening, and there was morning, the first day". The Brenton translation of the Septuagint has it the same way. Other translations are even more tilted towards a phrasing which supports the interpretation that the night was separate from the day. Here are a few. 

New Living Translation
God called the light “day” and the darkness “night.” And evening passed and morning came, marking the first day.
Berean Study Bible
God called the light “day,” and the darkness He called “night.” And there was evening, and there was morning—the first day.
Holman Christian Standard Bible
God called the light “day,” and He called the darkness “night.” Evening came and then morning: the first day.
Contemporary English Version
and named the light "Day" and the darkness "Night." Evening came, then morning--that was the first day.
Literal Standard Version
and God calls the light “Day,” and the darkness He has called “Night”; and there is an evening, and there is a morning—[the] first day.

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