Vitellogenin and Common Ancestry: Reading Tomkins

Competent ones don’t. Degrees are just a waypoint.

The DNA and protein sequences are His testimony regarding His creation.

I suggest that you take the time to compare and contrast them for yourself. You are grossly misrepresenting the nature and extent of the evidence for common descent without examining it when you employ vague terms like “shared” without bothering to witness for yourself.

Hi Theophilus -

I see in your writings a very poetic outlook on life…a vision of God’s grandeur, majesty, and creativity…and a sense that we are created for Him, to enjoy His presence and abide in His love. Those are wonderful qualities; thanks for sharing them.

It also seems that you are uninterested in scientific details. That’s OK; not everyone is. I would only urge you to consider Proverbs 18:17 as you mull over the issue or origins and creation:

The one who states his case first seems right,
until the other comes and examines him. (ESV)

When I was an avid believer in young-earth creationism, I did not heed this counsel of Scripture. Instead, when scientists, many of them Christian, attempted to advance scientific evidence for evolution or non-literalistic interpretations of Genesis, I would grab the nearest club. Then I would beat down their statements as ferociously as I could.

I hope you will learn from my mistakes; listen carefully to the evolutionary creationist side that gets shut out of many conservative evangelical gatherings. You may or may not change your position on how to interpret Genesis 1-3. I am, however, confident that you will reach the point where you consider “evolutionary creationists” as brothers and sisters in Christ who are doing their very best to glorify Him in a tough, complex world.

Peace,
Chris Falter

@dcscccc -

How are you doing, my friend? I hope you are feeling prepared in your heart to celebrate the death and resurrection of our Lord, which we commemorate this week. (And our brethren in the Orthodox churches a few weeks later.)

Thanks for clarifying this. You are stating now that humans have a vitellogenin pseudogene because, in the past, humans had a functional vitellogenin gene. I hope you will be willing to help me understand your position by providing a few more details:

  1. The human vitellogenin pseudogene does not now function in any way; correct?
  2. When did the vitellogenin gene stop functioning in humans? Thousands of years ago, millions, tens of millions, etc.?
  3. If another non-oviparous species (for example, opossum) has a vitellogenin pseudogene, it represents a formerly functional gene that no longer works. Correct?
  4. If a gene decays because it is no longer used, should we expect the pattern of decay to be predictable or unpredictable? In other words, should I be able to examine the human vitellogenin pseudogene, and predict what changes will occur in the next 10,000 years?
  5. Should I expect the vitellogenin pseudogene to decay in a predictable fashion in any other species besides humans?

As for the use of the word “may”:

You simply do not understand how probability works, and how scientists use probabilistic language.

I will try, one last time, to explain probabilistic language. Please, please, please, please try to pay attention. I think you will be glad you did. You may or may not agree with me about pseudogenes after our discussion, but at least you will understand what we have been talking about in all of the various threads where we have discussed probability. And that will be a good thing!

Suppose I were asked: will the German soccer (football) team win at least one game in the next 100 years? Based on what I know about soccer, I would say… absolutely! The probability of nothing but losses and draws over that period of time is infinitesimally small for the defending World Cup champions.

Now suppose I were asked: will the German soccer team win their next game?

That’s a lot harder question. Now we’re only talking about one game. One game is a lot harder to predict than 1000. So I would have to say “maybe.” That doesn’t seem like a very bold prediction, I know. But it’s all I could say. Anything can happen in one game.

Using evolution to predict pseudogene observations works the same way. Given a vast body of DNA evidence to work with, evolution predicts that many, many pseudogenes will be found. Evolution also predicts that the similarity of pseudogenes across species will correspond quite strongly to the phylogenetic nested hierarchy of the species. In general, the DNA sequence of a pseudogene in two closely related species should be more similar than the DNA sequence in two distantly related species.

However, it is a lot harder to predict what will be found with respect to just one pseudogene. Just like it is a lot harder to predict what will happen in just one soccer game.

The best way to examine the pseudogene evidence is to look at many of them, not just one. But it’s probably easier to understand when we look at just one at a time. That’s why this thread is dedicated to just one, the vitellogenin pseudogene.

Here’s what evolution predicts about pseudogenes, then:

  • Many pseudogenes should be present in the genomes of many species.
  • Whether a particular pseudogene will be found in a particular species is much harder to predict, however.
  • When a particular pseudogene appears in many different species, it should generally be more similar in species that are closely related, and less similar in species that are more distantly related.

Don’t give up hope, dcs! We can make progress if we work hard–especially if we listen to one another carefully.

Peace,
Chris Falter

P.S. I invite any biologists who are reading this thread to confirm or clarify what I have written about the predictions of evolution with regard to pseudogenes. Thanks!

This is correct. It is the precise mathematical pattern of differences that fulfills incredibly precise predictions.

We can be very confident that anyone trying to avoid this by using vague terms like “shared” and “similar” is only pretending to have familiarity with the massive evidence God has provided for us.

Hi Benjamin -

I greatly appreciate your help! And I pray you may experience the full measure of God’s grace this week as we remember our Lord’s sufferings and triumph.

It was not my assessment. Evolutionists have and do claim that since Man “shares” 97% to 98% of our DNA with Great Apes, we must conclude we descend from Great Apes. I make no such assessment. And my reason goes way beyond simply comparing the differences. It even included my assessment of my own ability to assess, compared with that same category of ability among the Great Apes. And I compare abilities to communicate the comparisons. Then I plug into the final equation what God has published about it. My God, not the Great Apes deity.

Why would I need to change? I already know from God’s word, that He utilizes either evolution, or a ministry of creation unknown to Man but assessed as Evolution.

At the top of God’s “evolution” H placed Man with the greatest of the Evolved Natural traits, i.e., Man makes tools, then evolves from them greater tools. He began with the simple club for making war, or the firs stick for making fire, and evolved his arsenal to the point He sent Men to the Moon. I call that Evolution in God’s Creature, Man.

And I am not a “young-earth” Christian. I do not picture God, from His revelation in Genesis, to have spent eons of time contemplating creation, and kajillions of eons gathering “Stuff” from which to make things.

God did not create time. Time and space are necessary for God to “BE.” “Place” requires Space, and “TO BE” requires Time. And no scripture ever says God made time and space. Simply that He “IS.”

The first thing God did, prior to creation, was “bring forth Wisdom” and Co-authored creation of what is. This can be found in Proverbs 8:22-31.

Proverbs 8:22 “The LORD possessed me in the beginning of his way, before his works of old.23 I was set up from everlasting, from the beginning, or ever the earth was. 24 When there were no depths, I was brought forth; when there were no fountains abounding with water.
25 Before the mountains were settled, before the hills was I brought forth: 26 While as yet he had not made the earth, nor the fields, nor the highest part of the dust of the world. 27 When he prepared the heavens, I was there: when he set a compass upon the face of the depth: 28 When he established the clouds above: when he strengthened the fountains of the deep: 29 When he gave to the sea his decree, that the waters should not pass his commandment: when he appointed the foundations of the earth:30 Then I was by him, as one brought up with him: and I was daily his delight, rejoicing always before him; 31 Rejoicing in the habitable part of his earth; and my delights were with the sons of men.”

Then God said “Let us make Man in our image.” This does not contribute to a triune deity, it contributes to careful reading of scripture.

Psalm 104:24 O LORD, how manifold are thy works! in wisdom hast thou made them all: the earth is full of thy riches.

Psalm 136:5 To him that by wisdom made the heavens: for his mercy endureth for ever.

Proverbs 3:19 The LORD by wisdom hath founded the earth; by understanding hath he established the heavens.

Jeremiah 51:15 He hath made the earth by his power, he hath established the world by his wisdom, and hath stretched out the heaven by his understanding.

When God continued to invest in Man, He taught him, and blessed him, and protected him, and nourished him, for He had made Man in His own image. He gave Man oversight of the creatures of the Earth, and geve him free will, and a knowledge of options, which gender selection, and choice, then told him to “Choose ye this day…” which brought about at least as much “Evolution” as Gene modification. It was the Modification of the mind that took Man to the Moon.

If you want to see evolution in action, look to the newborn infant. He begins by examining his hand. He will fist it, turn it about, taste it, smell it, gaze upon it until he knows everything there is to know, until one day he will use it to hold his bottle, or a rattle, or some toy, by which grasping affect, he learns to modify his living.

As He grows, and by examination and use, begins to see uses for toys, that were not the originally intended use, he is evolving before your very eyes. He is tool making, with every “thing” he can grasp in his hand, by his strength. Then he goes outside, and to the moon.

THAT is my understanding of God and His creating, and the “age of the earth” (at least as old as God less one second) kajillions of eons of time unmeasured by our standards, only recognized by Science’s ability to discover.

Science and God are not exclusionary one to the other. It was God who said "Doth not nature teach you…; and it was God who stated about the
Gods made by Men, “Them who by nature are no Gods.” This subtle suggestion tells us God is the only one who IS GOD BY NATURE. So why would he be at odds with Nature?

It is simply the ignorance of Man that promotes that insignificant babel.
God was first to point Man to nature as something to study and from which to learn.

Remember “Faith is the substance of things hoped for, by evidence of things not seen.” THAT is God suggesting you “bring out your magnifiers, of whatever nature you have made them, and study the things too small to see without them, and learn of Me.”

We begin to see ourselves and things within ourselves that are replicated in the small, in abundance, and marvel and wonder, and call it evolution. But it is simply God telling us and showing us that what is has always been, and what will be has already come before us. “No new thing…” we are told.

And God said it; I believe it; That SETTLES IT!

[quote=“Theo_Book, post:66, topic:4604”]
It was not my assessment. Evolutionists have and do claim that since Man “shares” 97% to 98% of our DNA with Great Apes, we must conclude we descend from Great Apes.[/quote]
Hello Theo,

See, there you go. You can’t even accurately represent the thing you’re arguing against.

You have made the assessment that it is wrong without characterizing it correctly nor examining the evidence that God provides.

One contrasts with differences. Comparisons are about similarities. There’s no evidence you have done either one before judging.

It seems that you have never examined the evidence before coming to a strong conclusion. Nor can you be bothered to accurately represent the “evolutionists’” position.

But you haven’t assessed the evidence.

Wouldn’t you need to make the comparisons and contrasts before communicating them?

[quote]Then I plug into the final equation what God has published about it.
[/quote]There’s a lot in the Bible about how carefully we are to weigh evidence before judging others. There’s very little about the generation of biodiversity. So why is the latter apparently so much more important to you than the former?

The sequences are God’s word on His creation, too, but you apparently ignore them. Why?

"There are small bits of data (pseudogenes) that are shared only by humans and primates, and found nowhere else in the animal kingdom.
[Evolution 2.0 by Perry Marshall, p.19 (bottom of page).

“The pseudogenes that humans and primates exclusively share are identical mobile DNA elements…A historian would naturally conclude common ancestry.”
[Evolution 2.0 by Perry Marshall, p.20 (center of page).

I differ with Marshall’s conclusion in that I would have said “Science” rather than “historian.”

The point remains the same. the popular conclusion would be, and still is, that humans and Apes share a common Ancestor. The fact that there is progress being made, in that some theologians are beginning to consider Evolution, and some Evolutionists are beginning to consider Theology, does not alter the equation by much, YET.

While I disown the assessment, I agree that God used Evolution in His creative effort. I preached about this prior to the turning of the century (in the 1980s), but was mostly ignored, occasionally debated, and often reviled. I also concluded “shared DNA” is due to a common creator instead of a common ancestor; because the dry land was separated from the sea, which shows a common source for DNA in the beginning, when creation took place.

As for your correction, that differences are contrasted, but similarities are compared; Both can be contrasted, both can be compared, depending upon the focus of your study. If I want to prove, I compare. If I want to disprove, I contrast. Others may do it differently. I do not insist it be said like I say it.

As for evidence I have made no such examination, none is required to reach my conclusion. My statement was one of theological discovery, contrasted with scientific conclusion. I disagree with a conclusion that disregards a scientific exercise in scriptural exegesis, but is interested only in the scientific research of a scientific interest.

As for the “Evolutionists position” remark, you reach an erroneous conclusion based upon a lack of bulk to my post that would cover such unimportant “Stuff” as my remarks were only concerned with pointing out the obvious, i.e., that the “scientific interest” was limited to the scientific experiment, and ignoring theological considerations.

I did assess the evidence, I just did not include the pros and cons in my post. They are not Germaine to the observation “Shared DNA does not prove common ancestry, but when common DNA source is discovered, it reflects a common creator.”

As for comparing and contrasting before communicating, I did that, and focused upon the discovery that agrees with my conclusion without including all that extemporaneous “stuff” of argument by which I reached my conclusion. It is not necessary to prove it in a simple statement about an observation of theological import.

I simply inserted my conclusion in response to a statement about “common ancestry.”

thanks chris. i will try to do it short.

  1. true.
    2)i dont know. it could by any one of them.
    3)(If i understand you correct) true.
  2. unpredictable. because some mutations can delete the entire gene or exons.
    5)the same

“may” its a may. you cant play with it.

so if we will find an example that contradict this, evolution will be falsified in this case? or because you add the “generally” again you avoid the falsification? if so then is not a true solid prediction.

[quote=“Theo_Book, post:69, topic:4604”]
I did assess the evidence, I just did not include the pros and cons in my post.[/quote]
What evidence? You assessed rhetoric.

Your claim is explicitly empirical, but you haven’t assessed the empirical evidence.

[quote]It is not necessary to prove it in a simple statement about an observation of theological import.
[/quote]Your observation was empirical, Theo, but you haven’t even looked at the evidence.

If you were on a jury in a murder case, would you reject all the empirical evidence in favor of testimony?

I will try to make it plain.

I was not attempting to prove anything, therefore, need no evidence. I was attempting to share an observation that made any evidence of “Shared ancestry” because of shared DNA to be a misapplied conclusion.

In other words, shared DNA does NOT Prove (Actually does not even suggest) shared ancestry; but rather verifies shared Creator. Since DNA comes from one common MUD pool, and all of creation comes from that common MUD pool, we should EXPECT DNA to be shared, by the commonality of creation.

This post had to do with how the Vitellogenin pseudogene could be identified beyond any reasonable doubt. Why does it matter? The Vitellogenin pseudogene is important largely because of mutations and deleterious errors within this identifiable pseudogene that happen to be shared between species that are not supposed to have derived from a common ancestor, which is simply inexplicable from the “shared Creator” standpoint. Even if all mammals started off with working Vitellogenin genes, it simply makes no statistical sense that a matching pattern of mutations would occur between all of these species. It goes against everything that we know about molecular biology, and to refer to a “common Creator” simply misses the point of the argument. Would a common Creator miraculously reach in (at some date later than creation week) and set up common sets of deactivating mutations over a few thousand years in a cross-species pattern that just happens to match that of the taxonomic nested hierarchies that have been established? Not only would this be referring to a miracle to explain away a pattern of evidence (making science redundant, which might be appealing to some), but it would be the very thing that God would need to do if he wanted to convince scientists of common descent (rather counterproductive in your scenario).

I can’t see how the vague, unquantifiable and rarely clarified “shared Creator” argument (given that it is usually expressed in no more than a single unqualified sentence, maybe “argument” is saying a bit much) addresses this at all. If it does address it in some unknown way, it will need much more elaboration and the hands will need to get dirty with the scientific details. Walk us through it. Others have more or less politely declined to do so, but maybe you have insight on how and why God would have implemented such an unfathomable procedure.

And you are not in a position to claim that you are discussing something purely theological and without need of scientific arguments when you claim to make empirical predictions (i.e. we would expect such and such a degree of similarity with a shared Creator). If you are discussing empirical predictions, then only scientific arguments will be meaningful. Otherwise we might as well just stick to “well, God can do whatever He wants, so why bother investigating or discussing it”, and close up shop, because this is where the argument starts trending as soon as you avoid the responsibility of grounding it in actual empirical details. There is a place for “God can do what he wants”, but not when it is used as an excuse to handily sweep all of the evidence off the table.

You’ve said something like this a couple of times and it sort of mystifies me. Where in Scripture or science or anywhere for that matter is it claimed that DNA came from a common MUD pool?! This one is new to me, which makes it interesting.

where is your calculation? or you dont have any?

Hi DC,

I’m afraid that our conversation ended a while ago (see above). I think it was wrapped up when you made it clear over a long series of posts just how much effort was needed to keep you from evading a single direct question from multiple people over dozens of posts.

I do not intend to restart the otherwise interesting conversation unless I can have confidence that an honest conversation can be sustained, one that actually leads somewhere because we carefully acknowledge valid points, we consistently follow out our own inferences, we clarify our own position or model in something more than than single sentence arguments and single word sentences, and we do not evade requests or questions in a systematic way. Unfortunately that that confidence has gone the way of the dinosaur (I think we can both agree on the way of the dinosaur, whichever model is used;-).

As I’ve said, I appreciate what you have to offer here in other ways, and I wish you the best, but this topic is closed with you for now.

Thanks

Before there was dry land and seas, the seas were not gathered, nor had the dry land appeared, until God called the waters together and the dry land separated out- “And God said, Let the waters under the heaven be gathered together unto one place, and let the dry land appear: and it was so.10 And God called the dry land Earth; and the gathering together of the waters called he Seas: and God saw that it was good.”(Gen 1:9-10)

Was this posted by mistake?

o.k. I think I see where you are coming from. Correct me if I miss the focus of your explanation. You seem to me to be saying God cannot do by simple utterance, what ONLY Science can accomplish. This is further supported by scientists who do not accept the creation account. For a “common creator/common creation” to account for all the vagaries of what is, requires a Scientist to assess, evaluate, and proclaim it to be not only possible with all that implies, but also give to the nth degree, the probability factors of a sustained program of decision-making changes that would result in what is.

Do I have it about right?

No, that is unfortunately a completely incorrect assessment of what I wrote. It also comes across as sort of curiously bitter and sarcastic with regard to science and scientists, but it’s always tough to tell with posts. Your response reflects so little of what I said (though it’s a slight improvement on your earlier response), that I’ll have to assume that you did no more than skim my post. You have posted a response as though I had written an extended rant about how limited God is and about the awesome creative potential of science and the infallibility of scientists (I don’t remember writing a post of this character), and you have not even given a cursory consideration of actual content of the argument.

That’s sometimes known as a bad start.

Yes, I’m sure God has carte blanch to do as he wishes. No I’m pretty sure that scientists are not semi-divine infallible beings. That said, I find it unlikely that God would miraculously intervene specifically in order to create a pattern of mutations that looks like what would be produced by common descent (common design is mute when it comes to patterns of deleterious mutations). If common descent didn’t happen, then this would seem a little pointlessly dishonest, and would hardly reflect what might be expected based on the conclusions of a couple of thousands of years of theology. Until you bother to look carefully at the argument, you simply won’t see this. So sure, granted, God may have done it in 6 days using separate creation, but if true, the pattern is highly misleading and we have a major theological problem in place of a scientific problem.

Granting your premise, why do you think, as a student of God’s character, that He went to the trouble of creating or modifying DNA, including pseudogene mutations (inversions, frameshift mutations, premature stop codons, etc.) according to a pattern that is predicted only by common descent?