Vitellogenin and Common Ancestry: Reading Tomkins

Faith & Science Conversation
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[quote=“bren, post:80, topic:4604, full:true”]
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. [/quote]

Funny! THAT is what I was going to write about your responses to my posts.

I began with one simple assessment; stating that shared DNA does not necessarily indicate common Ancestor; but rather demonstrates common Creator.

From there, it has escalated to demands for my “proofs (or evidence”)
And I think it is becoming foreign to both of us.

That was because I was not responding to your argument, I was responding to one statement, which was a standalone post, if I correctly recall.

My opinion is “Common descent” has never been proven to be the
“only” way to account for the pattern. I would question any such
“prediction” as not a prediction, so much as a staged result. Just because a scientist sees an alteration in a segment of creation, that does not prove “prediction” even if the scientist published what he was looking for prior to finding it. THAT is simply a natural order of pattern variation.

To me, “Predicting” would be for a scientist to tell what form Humans will be in a future environment that requires millennia for development; and he leaves a record of his prediction based upon his analysis of pattern adjustment in his own day that he thinks justifies his particular prediction, and then millennia later, scientist look at his data, and find examples in nature, precisely as he has laid it out in his prediction.

Anyway, I do not care to chase a rainbow I thought was in the thread, and I find I interrupted a train of thought rather than added to it, for which I heartily apologize, and will simply move on.

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My original insertion was simply based on the observation that you did not apparently understand the thing you were criticizing; the scientific arguments for common descent. You showed a disdain for something without showing that you had any grasp of the argument that you were rejecting. Maybe you did grasp the argument, but your comments strongly suggested otherwise. I briefly tried to re-frame the issue in a way that might be accessible, but if it wasn’t, then I’m sorry that your time was wasted. This sense that you did not really have a clear picture of the science or the reasoning involved has been reinforced by statements about DNA from a common mud pool, the symbiotic relationship of our respiratory system being independent of our DNA, and interesting views on what does and what does not constitute a scientific prediction. On the whole, this gives me the sense that you are picking up bits and pieces of second and third hand science without the background to integrate or question what you hear.

You are certainly neither the first nor the last to have very strong and very marginal opinions on scientific matters without having the obvious strong scientific background that may justify such assurance, but I always find it surprising when such a difficult to account for position is combined with a tendency to stay aloof from the specifics of the arguments, speaking in bold generalities instead of working through these questions step by step. This is of course a decision that is yours to make, but it makes the assurance of your opinions on scientific matters pretty unaccountable. Of course, I guess the best solution is that for many, and maybe for you, it is borrowed assurance, based on years spent hearing creationist experts confidently describe evolution as an empty and unscientific position without taking the Berean position (yes it can work for something other than scripture) of doing background and reference checks on their position.

Still, the point of this site is to engage with such views and work through them. If you have come to drop off your disdain for some scientific position while ducking the opportunity to actually engage with the logic of your own and your opponents view, then yes, maybe you are chasing something of a rainbow.

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[quote=“bren, post:82, topic:4604, full:true”]
My original insertion was simply based on the observation that you did not apparently understand the thing you were criticizing; the scientific arguments for common descent. [/quote]

I showed no disdain. I offered an alternate solution, Common DNA source, as coming from a common creator rather than a common ancestor. How is that disdain for science? Doesn’t science offer alternative solutions in their research? Please look at my first post in this thread and point out the disdain.

[quote=“bren, post:82, topic:4604, full:true”]
You showed a disdain for something without showing that you had any grasp of the argument that you were rejecting. [/quote]

I was not responding to the argument of the thread. I was offering an alternate to the issue that was prevalent in one post; that shared DNA demonstrates common ancestry.

I was not addressing the argument. I have not made claim to addressing the argument. It was the conclusion I disagreed with and have stated so several times now. Why do you keep reinserting the argument into the discussion?

The question between Darwinian Evolution and Intelligent Design has been settled in ID’s favor, so I fail to see where it is still relevant.

My time was not wasted. I enjoyed your posts, and your reasoning. I do not have to hear it like I say it and think it like I think it to recognize true belief and effort and appreciate a sincere effort to convince another way of thinking. I appreciate your time invested to understand what I was trying to convey, even though I seem to have done a sad job of it.

That is because the issue under discussion was not about symbiotic relationship nor was it about Intelligent Design. I have thrice explained the tiny segment of interest I addressed in my first pot, and the concurrent misunderstanding developed by your correction.

Nope! Missed again. I offered a simple correction to what I considered an erroneous solution to the issue as I understood it. My response was not only limited, it was OBVIOUSLY limited to one segment of the issue, and that had to do with DNA shared in Humans and Apes due to a common Creator, rather than a common ancestor, such as I read in your post. THAT was ALL my response entailed. The rest is your projecting.

Nope! The rainbow I was chasing was a mutual appreciation for an exchange of concepts about the affect and result differentiated by dependence upon evolution/ancestor and creation shared DNA source.

No disdain, no shirking of research, no lack of mental acumen… Just limited focus on one tiny sliver of your remarks.

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It seems to me, @Theo_Book, that you are perhaps claiming merely that the commonality of DNA in life as we know it is evidence of a common creator. If I am understanding you correctly, you are not at the same time making a claim for or against evolution as a scientific discipline, per se; rather, you are making a claim against evolutionism as a guiding principle of life and values. That is, you refute an atheist philosophy that goes beyond the bounds of science and makes claims about the ultimate meaning of life (or lack thereof, in that view).

I trust you have become aware that no one is this thread is pushing such a view of evolution; we have all been viewing it as the mechanism by which God created life as we know it today.

What we have been talking about is how the arrangement of DNA nucleotides can be used to infer strong conclusions about the life God created. Fundamentally, the claim that @bren, @benkirk and I have been making is that the details of DNA arrangement can be used to infer common ancestry.

Before you start objecting, please take a deep breath. There, that’s good. Now take another deep breath. Ready? Consider this: every day, court rooms in America accept the similarity of DNA as a measurement of ancestry.

Suppose there’s a paternity lawsuit. A scientist measures the similarity of the DNA from a child with the DNA from some adults, and infers how close (or distant) the relationship is between the child and the adults. Greater similarity = closer ancestry.

Suppose there’s a dispute over the estate of someone who was buried many years ago. There is no reason to dig up the interred remains of the deceased for tissue samples; instead, a scientist can take DNA samples from the plaintiff and defendant to determine whether they have a close common ancestor (such as a grandparent).

Moreover, similarity of DNA can be used as a measurement of ancestry going back many thousands of years. My sister-in-law sent a DNA sample to 23andme to see where the family’s genetic roots lie. The 23andme report described the family ancestry, dating back several thousand years.

What biologists are doing is simply extending the DNA similarity analysis farther back, and finding ancestries even more distant.

Hope this helps you understand the topic a little better.

Take care, and may you enjoy the hope of Easter this week!

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Hi @dcscccc

Hope you are doing well this week.

Okay, now we have something to work with. When a scientist describes a decay process as fundamentally unpredictable…

and 2 independent instances of that decay process are occurring simultaneously…

there should be no relationship between the outcome of the two processes.

If a paint bomb goes off in a crowd, some people will get hit by paint in the right eye. Others will get hit in the left shoulder. Others will get hit on the right knee. The variety of outcomes occurs because the distribution of paint from a paint bomb is quite unpredictable.

If everyone gets hit in the right eye and nowhere else, though, a scientist would make a very strong inference that the distribution of the paint was not a stochastic (unpredictable) process. Instead, a scientist would infer that something–perhaps a very sophisticated micro-targeting system–was directing the paint only toward the right eye of bystanders.

By the very definition of predictability, then, the creation model must expect that the outcome of the unpredictable, independent decay processes for a pseudogene in unrelated species would demonstrate no pattern of similarity. If the decay is not too extensive, it would be possible to identify a particular pseudogene in the species; but the manner in which the decay occurred should be different in unrelated species. One of the species might have a stop codon where the other has a frameshift, for example.

Do you have any disagreement with this, @dcscccc?

The only thing I can conclude is that you don’t even bother to read my explanations. I put a lot of work into what I write. And you are not even trying to understand it! It appears that you do not consider what I have written to be worth thinking carefully about. You are not treating me as I treat you, dcs.

Anyway, the Lord Himself created the universe in such a way that many processes are probabilistic. The decay rate of an atom. The kinetic energy of gas particles. And the decay patterns of pseudogenes.

Since God created the universe in this way, I fully support the efforts of scientists to use the laws of probability–indeed the very laws that God stitched into the fabric of the universe!–to understand that creation.

Gravity works even if you don’t understand it, dcs. And the probabilistic decay of DNA in pseudogenes works even if you don’t understand it. But you would be happier, and wiser, if you would at least attempt to understand it.

Actually, evolution would not be falsified at all. When 10,000,000,000 observations confirm evolution and only one seems to contradict it, you need to investigate further before you just discard the 10,000,000,000 observations. Further investigation could reveal measurement error, or incomplete lineage sorting, or plain old stochastic drift. A real biologist could probably provide many more explanations for such a case.

Hope this helps you understand the topic a little better.

Take care, and may you enjoy the hope of Easter this week!

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Chris, you’re doing just fine! (as is Bren). Thanks to both of you for taking the time to work through this.

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Hello Theo,

I don’t see what you write as plain. It appears that you are using a very different definition of “shared” than the rest of us are using. We are talking about sequences.

By the way, science doesn’t prove anything–all conclusions are provisional. That’s why it’s so powerful.

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not always true. some places in the genome are hot-spots. but its also possible that the mutation rate is changing over time and therefore we cant always predict how much different we will see in a 2 shared pseudogenes. also remember that it can be the result of convergent loss. so in this case you also cant predict how much different we will see.

i actually read all of them. i just dont have enough patience to struggle with english. so i try to make it short and focus in the main argument. and the main point is that evolution doesnt predict that its always be the case.

so you admit that evolution cant be test or falsified? or just in this case but generally we can test it?

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I am using

[quote=“benkirk, post:87, topic:4604, full:true”]

Hello Theo,
I don’t see what you write as plain. It appears that you are using a very different definition of “shared” than the rest of us are using. We are talking about sequences.[/quote]

How would you suggest I make it plainer than my reference to “Shared DNA indicates a common creator rather than a common ancestor?”

I am not the one who needs to be convinced; scientists are. Evolutionists and Intelligent Designists are debating the issue of Intelligent Design vs. Evolution and the Evolutionists still insist that Shared Dna between Apes and Humans proves evolution and human descent from Great Apes.

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So the refrain that I’m catching here is that you were only presenting your own view that the common Creator hypothesis (CCH) offers an equally or even more valid explanation for similarity than common descent. You consider that the common descent explanation is an “erroneous solution to the issue” as you understand it. Your observations are further only limited to “DNA shared in Humans and Apes”. You make no further claims, and anything that I say that goes beyond this is my projecting (love that word).

As it happens, and you may have missed this, I was discussing exactly this, but I was being even more specific. Not only was I discussing similarity between chimps and humans, but I was discussing the similarity of a particular set of mutations in a particular pseudogene (while observing that my counter-argument works well beyond these limits).

Why does this very specifically respond to your observation? As I clearly pointed out, it is simply because the common creator hypothesis does involve a prediction here:

The prediction is that if God created Vitellogenin in all mammals (for some unknown reason), explaining the existence of the Vitellogenin pseudogene, then wherever the gene becomes a pseudogene, it will be mutated in an independent and stochastic (random, if you’d like) manner in each kind - this is standard molecular biology. Horses and Zebra’s would therefore likely have a similar pattern of mutations in the pseudogene, since they have common ancestors that already presumably have some some of the mutations that they would pass on to both species. Chimps and humans, on the other hand, having no common ancestor at all because they are different kinds, would have a completely independent set of deleterious mutations. This is a very specific prediction based on up to date determinations of the extent of biblical kinds according to baraminology, but the idea would work regardless of how kinds are defined (and it could even be used to define the limits of kinds - take note creationists).

Mutagenesis (the generation of new mutations in DNA sequences) can occur in a virtually astronomical number of ways in each sequence within each kind, so the chances that there would be a recognizable common pattern of mutations in Vitellogenin between two kinds is virtually nil. For this reason, without a testable and detailed auxiliary (additional) hypothesis it happens that the CCH entirely fails to explain the pattern of similarity that we are discussing, which seems to exist very clearly between kinds. You need to add a hypothesis (sort of a pericycle); why should we get this common pattern of mutations, wholly against the predictions of standard molecular biology? It is not that there can’t be such an auxiliary hypothesis, its that there isn’t one; no one has spelled one out; not here and not anywhere.

I suggested that God could choose to control the mutation process in this and only this case for some reason. Since mutagenesis does not work this way and since a scientifically grounded (aside from common descent) reason has become rather unlikely at this point given our knowledge of molecular biology, this is why I tried to think of some theological motive for forcing mutations into a pattern that just happens to also be predicted by common descent. The reason a theological explanation fares no better is that it needs to explain why God would miraculously force a pattern throughout nature that just happens to be very specifically and uniquely predicted by something that is entirely false (common descent), misleading intellectually honest scientists (including Christian scientists) everywhere and for good.

This addresses your main and your first point very directly, without even going into whether or not you have a background that enables you to assess this (frankly, it wouldn’t matter, since this isn’t exactly complicated biology). Your only point was: here’s an alternative that no one seems to want to look at and my point was: no, it doesn’t predict what you are claiming at all, it predicts a very different pattern that we simply don’t see.

Chris did a very nice job of explaining the idea with his paint bomb illustration and I think you should make use of this in place of my explanations. Either way, it remains true that you have brought forward an alternative hypothesis that fails to do what you claim for it where common descent explains why these patterns are shared and why they sort into nested hierarchies in the simplest manner possible.

I explained much of this above, and what I find strange is that you are calling me out as though I had failed to even notice the point you were making.

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Hi @Theo_Book

I believe you have inadvertently overlooked this post that I directed specially to you. My gift! I think you will find the explanation of the DNA evidence to be very illuminating.

Grace and peace,
Chris Falter

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Hi @dcscccc

Hope you have been enjoying God’s grace since we last conversed.

You dramatically misunderstand convergent loss. Convergent loss means that independent lineages experience loss of similar genetic functionality under similar selection pressures. It does not mean that the loss of genetic functionality occurs as a result of identical mutations.

Here is an example of how convergent loss happens as a result of differing mutations, from the research report “Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor”:

We conclude that parallel genetic evolution of separate metastatic sites with different PTEN genomic alterations leads to a convergent PTEN-null phenotype resistant to PI(3)Kα inhibition. [my emphasis]

Convergent loss demonstrates plenty of randomness; it in fact illustrates precisely what @bren and I have been saying throughout this thread. The evidence confirms the prediction of evolution.

Thanks for the affirmation, dcs, I appreciate your explanation. I would suggest that you use an online service like translate.bing.com or translate.google.com. Enter what you want to write in your native language, then ask the service to translate it to English. Then edit the generated English to correct the occasional error. The services are quite good, actually. I have used them myself to translate from English to French, although I find I do need to edit the output a little bit to make it a little more au courant.

Not in the least. I am simply stating that you need to use a test that recognizes the stochastic, probabilistic nature of what is being studied. And to do that, you need to understand statistical methods. You seem not to have understood what I was trying to illustrate by the German soccer team analogy. Here’s a suggestion: Please state how the German soccer team analogy applies to the discussion of DNA sequence analysis. Do your best. You will learn a lot from the effort. If you misunderstand something, you have friends here to help you learn.

I want to offer two more statistically-based reasoning exercises for you. If you will answer these questions to the best of your ability, perhaps we can really make progress together.

(1) [A thought experiment] Physicists have declared that Uranium-238 has a half-life of 4.5B years under conditions prevailing on our planet. Geologists use this half-life to calculate the age of geological formations in terms of billions of years.

You decide to test the half-life of U-238 by observing 2000 atoms of the substance. After 4 years of observation, you observe one atom decay into Thorium-230. You stop your observations, and perform a calculation of how long it would take for one-half, or 1000 of the atoms, of U-238 to experience radioactive decay:

1000 atoms x 4 years per atom = 4000 years

So you conclude that the half-life of U-238 is really a million times lower than the physicists have been claiming. And in turn, all of the geologists need to reduce their estimate of the earth’s age by a factor of a million; the earth must only be a few thousand years old.

Is this a good scientific approach? Can you overturn the physicists’ estimate of the U-238 half-life on the basis of an observation of the decay of a single atom?

(2) The second example comes from a 2014 study of the relationship between street lights and crime in Chicago. On average, the crime rate increased 7% when street lights were not functioning in a neighborhood. There was, however, one neighborhood where the crime rate decreased when the street lights were not functioning.

Should officials in the city of Chicago conclude, on the basis of that one neighborhood, that functioning street lights actually cause crime to increase? Since non-functional street lights were associated with reduced crime in that one neighborhood, should the city of Chicago shut off the street lights in all the neighborhoods in order to reduce the crime rate? If not, how can we explain that one neighborhood that exhibited a different relationship between lighting and crime than everywhere else in the city?

Once you have demonstrated an understanding of these examples, I think you will be able to understand what @bren and I have been saying about similarity of DNA sequence in pseudogenes. So please try to answer the questions about the half-life of U-238 and Chicago street lights. Thanks!

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[quote=“Theo_Book, post:89, topic:4604”]
How would you suggest I make it plainer than my reference to “Shared DNA indicates a common creator rather than a common ancestor?”[/quote]
By defining “shared” explicitly and mathematically.

[quote]…the Evolutionists still insist that Shared Dna between Apes and Humans proves evolution and human descent from Great Apes.
[/quote]This would be more credible if you could provide a quote and context stating precisely that.

Is it ethical to put words in the mouths of other people?

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and you dramatically misunderstand me. i doesnt said it will be similar in the base level, but just said that if one gene is the result of convergent loss, then we cant predict the level of similarity we will see.

i understand this very well. i also understand that you dont want to check if evolution can be test. and its fine. have a nice day chris.

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Hi @dcscccc

Ok, thanks for clarifying. You seem to be saying that in a creationist model, there should be no similarity in mutations of DNA sequence of unrelated species, if I am understanding you. Is that correct?

Actually, in many of your posts you have demonstrated a great lack of understanding about the simplest principles of probabilistic modeling.

Moreover, you have just demonstrated that you are not interested in learning anything about probabilistic modeling. I spent a lot of time trying to come up with scenarios that illustrate probabilistic modeling just for you, my friend dcs. But in spite of my hours of effort, you could not be bothered to respond to the U-238 decay scenario or the lighting/crime scenario. Why not, dcs? The appearance is that you do not even want to try to understand.

I officially give up on trying to help you, dcs. All of the evidence from this conversation and from our previous conversations is that you have a complete lack of desire to understand how probability works and how it applies to DNA sequencing. I have better ways to spend my time. If, however, you should ever change your mind, I will still be glad to help. But the next move must be on your part, not mine.

That’s a complete falsehood, dcs. I have stated repeatedly that evolution provides a testable model of DNA sequences in pseudogenes, based on probabilistic modeling. I have even provided citations to the predictions made by biologist Dennis Venema.

The fact that you are unwilling to even attempt to understand probabilistic modeling means that you will never understand why those predictions result from the theory of evolution.

Until you work on understanding probabilistic modeling, you will never understand even the kinds of predictions the YEC theory would make about DNA sequences in pseudogenes.

Until you understand probabilistic modeling, you will certainly not understand how to test the predictions.

Just because you don’t understand what I said, and how it supports testable predictions from the theory of evolution, doesn’t mean I don’t want to check if evolution can be tested. It only means you don’t understand.

I pray you might enjoy every facet of God’s love and power this Easter.

Peace,
Chris Falter

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i actually refer to the evolution model.

as for your u-238 example- my answer is no. because one case cant falsified a lots of other cases. now when i answer your question i think you should answer mine- how we can test if evolution is true or not? thanks.

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Multiple people have already answered this question for you on repeated occasions. If you still don’t understand, and are honestly interested, a link to a course on evolutionary basics is included below. Not understanding is different than not agreeing. It is fine if you do not want to accept the answers that have been given as valid. But please stop wasting people’s time with questions that have already been exhaustively addressed on your behalf. That is just inconsiderate.

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Also, you need to seriously consider the possibility that you’re the one who’s not getting it, rather than everybody else.

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Hi @dcscccc

Every time I think that you might have provided enough information to formulate a YEC model for DNA sequence analysis of pseudogenes, you repudiate the formulation. You have also ignored repeated requests to describe a YEC model for DNA sequence analysis of pseudogenes. You are of course under no obligation to advance or confirm a model. But you cannot win a race if you do not start. The people you are disagreeing with have formulated a testable model. You cannot expect to convince anyone that you have a better idea if you cannot even formulate your idea in a testable way.

Actually, you are still a very, very long distance from displaying an understanding of how probabilistic modeling can be used to analyze DNA sequence similarity in pseudogenes. My logic about U-238 seemed impeccable–I observed an atom, it decayed in the time period of 4 years, and I applied a simple math formula. Given that science needs to explain all observations: how can that observation of one atom be consistent with a half-life of 4.5b years?

Simply stating that it’s one observation doesn’t mean it can be ignored. There has to be something about that observation that can be explained in a way that is consistent with a half-life of 4.5B years. If you can provide that explanation, dcs, you will have understood an important aspect of probabilistic modeling. Until you can provide such an explanation, my friend, you are still in the dark.

You still need to answer the other question, too, since it addresses one other factor in the analysis.

And finally…

I already answered that question earlier in this thread. You’re welcome.

Happy Easter!

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and i already answer this. here it again:

“the key word here is “may”. so its actually what i have said- even if we will find a working vit in some mammals evolution will not have any problem. its not a prediction. even in an opposite evidence- that we will not find any vit remains, also predict by evolution. even the paper could not find some vit genes in some species. so there is no a real prediction here. for both creation and evolution models.”-

now, if you will say that one case cant disprove the whole theory its ok. but then you cant call it science. because any case when we will find an evidence against the theory you will say that its just one evidence against many. do you see the problem?

now- i also answer your question about the u238. if we will find one c ase that contradict a lot of other cases it will not disprove the entire method because it may be the result of a unique process or bad use of the method. but again- where is the limit? one bad dating? 10? 50? if its science- we need to offer a limit.