It is fairly easy to refute, the text of Genesis 4:1 says.
"And Adam knew Eve his wife; and she conceived, and bare Cain, and said, I have gotten a man from Yahuah."Making it clear Adam is the father, it's the exact same way Seth's conception is described in verse 25.
Saying Eve and the Serpent had sex is based on a laughably bad Augustinian view of Original Sin. Sometimes people who don't even believe The Bible will tell me "The sexual subtext of the story is obvious, Snakes are Phallic shaped". Except we're never told this was a Snake, the Hebrew word translated Serpent here could refer to any Reptilian animal, or even Amphibians when you include sea serpents. Some Bible passages refer to flying Serpents which I believe were Pterodactyls. Snakes are not the only Reptilians that crawl on their bellies, most still around today do. Leviathan is called a Serpent twice in Isaiah 27:1. And even outside The Bible the imagery of the Egyptian Ogdoad has the Females be Serpents and the Males as Frogs.
Some people want to say the words for "Beguiled" in Genesis 3:13 and 2 Corinthians 11:3 are inherently sexual terms. That is absurd, those Hebrew and Greek words mean deceived, nothing more. The Greek is Strongs 1818, the Hebrew is Strongs 5377. Both are used in non sexual contexts.
They abuse how the context of Paul's verse talks about Virginity. Paul is not using Virginity literally here, as he's talking about the Church as the Virgin Bride of Christ. Eve was most certainly not a Virgin anymore when Genesis 3 happened, her and Adam were already commanded to be fruitful and multiply, and Genesis 2 ends with them being made one flesh, that's terminology about sexual union. The context of what Paul is talking about is the Mind being corrupted, not the flesh.
Lots of New Testament verses are using terms like "son of" and "father" and even sometimes "Seed" in a not literally biological sense, because a major theme is Gentiles being adopted into Israel. In John 8 Jesus calls people Abraham's Seed and then says that they are not of Abraham but of their father The Devil. But 1 John 2:12 which they abuse doesn't even use the word "son", it just says Cain was of the Wicked One, the same way we are of Christ.
This theory is dependent on a lot of Extra-Biblical sources. Interestingly enough the Targums they cite they are not citing well either. They take Targums that sound like maybe they're saying Eve "knew" an Angel, but that go on to clarify that Angel was the Angel of The LORD which is Biblically a title of the Pre-Incarnate Jesus.
One Targum says Cain and Abel were twins, which is more compatible with the text of Genesis 4 then I thought at first. But if a Supernatural entity was involved in this in addition to Adam, that would be Yahuah based on what the text says.
And you really shouldn't cite the Proto-Evangelion of James if you're not a Catholic, it teaches early forms of certain Catholic Marian Doctrines. Either way that text is maybe an early example of thinking something Sexual happened, but gives no support to saying The Serpent fathered Cain.
Mostly the Two-Seedline theory comes from Gnostic texts like the Gospel of Philip. And even today these Seed-Line theorists are teaching Quasi Gnostic stuff, not proper 'the Serpent was Jesus and Yahweh was Evil' Gnosticism, but very Quasi Gnostic by saying that Adam and Eve only became physical Flesh after the Fall, like what Origen may have taught. Adam says after Eve is created in Genesis 2 that she is "Flesh of my Flesh and Bone of my Bone", they were not merely Spirit beings.
I've seen one argue for the Adam of Genesis 1 being a separate Creation, an idea I've dealt with elsewhere. But like others using this for a compromise with Evolution he has it flipped around. It would be the Genesis 1 creation that is merely Spiritual. Genesis 2 describes the element Adam's Body was formed from so it's clearly of a physical body, and in verse 23 Adam calls the Woman flesh of his flesh and bone of his bone. The fact that Adam is in a plural form in the Hebrew text of Genesis 1 is pointed out by them ignoring the context that Hebrew often uses the Plural Suffix for individuals as a sort of emphasis.
Now I can see the logic behind looking at Genesis 3:15 where Yahuah is talking to The Serpent.
"And I will put enmity between thee and the woman, and between thy seed and her seed; it shall bruise thy head, and thou shalt bruise his heel."And concluding there must be a Serpent Seed-Line somewhere. The Jewish view has always been that the Seed of the Woman is Humanity in general, all Eve's descendants. I don't view that as contradicting it being largely fulfilled in Jesus, but regardless no New Testament author quotes Genesis 3:15 as Messianic So I can see viewing the Seed of the Serpent as a similar rival species. But it contradicts the whole point of this same verse if they are also descendants of Eve.
It could maybe make sense to suggest they are descendants of Adam but not of Eve, but certainly not the opposite. Though there is no solid Biblical basis for that theory either, I shall speculate none the less, but I'll do so on the Comparative Mythology Blog.
What I certainly do not believe is that any Seed of the Serpent exists in the Gene Pool of contemporary Homo-Sapiens. If The Antichrist is a Human-Serpent Hybrid, it'll be a trait that is completely unique to him. But I've come to doubt the assumption that the Seed of the Serpent has anything to do with The Antichrist, Revelation 13 and II Thessalonians 2 both call him Anthropos, meaning he's a normal Human Being.
With the Beast we know the seven heads and ten horns imagery represents more then one individual being involved in what The Beast represents, even if one particular individual is more important then the rest. So I've come to think the seven heads and ten horns of The Dragon are the same, the Dragon is The Serpent and it's Seed.
A lot of people think Genesis 3:15 is unique in implying a Woman can have Seed. While it's difficult for us today to accept using the same word to refer to both the male and female contributions to reproduction because of our modern scientific classifications, that is what The Bible does in more then just Genesis 3 and Revelation 12:17. Ishmael is refereed to as Hagar's Seed in Genesis 16:10, and in Genesis 24:60 Rebeca is told that her Seed shall be thousands of millions (that's Billions).
Now it's possible you could argue that these verses don't contradict Seed meaning specifically Sperm by saying that Seed a male produced becomes a Woman's once it's entered her. Leviticus 12:2, 15:18, and Numbers 5:28 could support that., as could Ruth 4:12 and 1 Samuel 2:20. In 1 Samuel 1:11 the "child" in "man child" is the Hebrew word usually translated seed, as well as the use of "child" in Leviticus 22:13.
But once you allow that, then that also becomes a viable explanation for Genesis 3:15's Seed of the Woman. In any explanation for how a Woman having Seed makes sense, all children of Eve would be her Seed regardless of the Father. So in order for the Serpent's Seed to be separate, it has to not descend from Eve.
I believe strongly in the Virgin Birth as shown by my Almah post, but I've come to disagree with using Genesis 3:15 as part of that doctrine. The Seed of the Woman is in a sense all descendants of Eve, Jesus as the Messiah is simply the key Son of Adam and Eve through whom this destiny is fulfilled.
In Romans 16:20 Paul says that God will bruise Satan under our feet. And Jesus said we will tread on Serpents and Scorpions in Luke 10:19.
In Genesis 4:25 Eve says that Elohim appointed her another Seed instead of Abel whom Cain slew. Something I'm sure many Serpent-Seed theorists point to. But it shows that Eve was referring to all her offspring as her Seed. At the start of the chapter she gives Yahuah more direct credit for Cain then she did for Abel.