Vitellogenin and Common Ancestry: does BioLogos have egg on its face?

Faith & Science Conversation
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Dennis,

Great to see you’re revisiting this! And I really appreciated the work you’re doing at Biologis btw.

That said, have you ever seen this creationist article in vtg pseudogenes?

http://www.truthinscience.org.uk/content.cfm?id=3113

I’ve quoted the relevant portion below:

"Their research identified vitellogenin pseudogenes in the previously published human and dog genome. A pseudogene is essentially a non-active version of a previously functional gene that has been switched off. In the case of the vitellogenin genes, Brawand and his group found that there were “premature stop codons and frame-shifting insertion/deletions” in genomic regions equivalent to the active vitellogenin genes found in the chicken. Are these pseudogenes a relic of mammalian evolutionary history? Brawand and his colleagues think so but is their another explanation?

Do placental and marsupial mammals need the ability to produce egg yolk at any stage in their life cycles. The answer is an emphatic yes! In the paradoxical words of Brawand and his group:

Marsupials also have a placenta, originating from the yolk sac, but the marsupial oocyte [egg] contains considerably more yolk than that of eutherians, which is virtually devoid of it. The marsupial yolk reserve is assumed to be essential during the earliest development of the embryo, complementing the uptake of uterine secretions by the yolk sac, prior to shell coat rupture. However, the content of marsupial yolk is not well known.The fact is this; all mammals require yolk at some stage in development. In particular, all placental mammals produce eggs that require yolk for nourishment prior to the establishment of the placenta. In the words of LM Baggott in his book entitled Human Reproduction: The eggs of mammals contain relatively little yolk compared to the eggs of other vertebrates. However, yolk is present in sufficient quantity to sustain the development of the embryo through the period of cleavage … In placental mammals, including of course humans; cleavage takes place as the embryo passes down the Fallopian tube towards the uterus. During this period, the embryo draws upon the reserves of yolk in the dividing cells. After implantation, has taken place in the uterus and until birth, energy and raw materials come to the developing embryo from the maternal circulation [from LM Baggott (1997) Human Reproduction Cambridge University Press page 33].
This fact might allow an alternative explanation for the presence of vitellogenin pseuodogenes in placental mammals. In fact, seen in this light, pseudogenes may sometimes be active genes…"

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[quote=“dcscccc, post:17, topic:4405”]

ok. so if for example fish was similar to human then chimp (from dna prespective) then you need to believe in this case that fish are closer to human then chimp from phylogenetic prespective? i doubt on it.[/quote]

You are appealing to magical, hypothetical evidence that does not exist. How are we supposed to make progress in our discussion?

The distance from fish to human DNA is far, far greater than the distance from chimp to human DNA. If you can find any published evidence to the contrary, please let us know so we consider it carefully.

Convergent loss does not begin to address the GULO gene evidence for evolution. The way the gene is disabled varies among species:

  • The human GULO gene remnant is very much different from the guinea pig GULO remnant.
  • It is closer to monkey GULO remnants.
  • It is even closer to the chimp remnant.

You assert that the YEC/ID creationist theories predict that the GULO gene would be disabled in a variety of species that are subject to similar natural selection pressures. However, your assertion does not address the subject of discussion. Not even close.

Dr Ex-YEC, argon, and I have been talking about the fact that there are millions of different ways to disable the GULO gene by random mutations. If chimps and humans are not related phylogenetically, there are astronomical odds against chimps and humans having the same set of disabling changes–given that there are so many millions of different sets of disabling changes.

Does that make sense?

Unlike YEC and ID creationism, evolutionary creationism predicts that the GULO remnants should become more dissimilar as phylogenetic distance increases. Which is what we observe in the DNA evidence.

From the beginning of this discussion, my dear friend dcscccc, you have not given any evidence of recognizing what is being argued by evolutionary creationists, and how it relates to the DNA evidence. I have tried to explain this as clearly as possible in this post. But a far better explanation and detailed discussion can be found in this video by Stephen Schaffner of the MIT/Harvard Broad Institute. He has a Ph.D. in particle physics from Yale University, and specializes in the genetics of natural selection. He also shows up in the BL discussion forums from time to time under the moniker “glipsnort.”

Please, go and view that video and think about the evidence he presents.

We would expect, in a stochastic process that takes place over hundreds of millions of generations, that the shape of a proximity estimator across a large set of predictors would vary. In other words, the rate of variation is not constant across all genetic regions. Therefore, the generalized situation you describe does not pose any difficulties to the theory of evolution.

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I’ve already had a lengthy discussion with dcscccc about GULO. See here, for example.

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Thanks for providing the interesting link to Wood’s blog. Unfortunately, the link is missing the final “l” in “html.” This is the correct link.

Grace and peace

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so if 2 species are much more similar from morphological prespective then the third one, therefore the third one cant be closer from dna prespective?

are you sure? how many disabling changes we are talking about? remmember that we talk only about identical changes (the same base\amino acid).

. again- about 1\3 of the gorila genes are more similar to human then chimp. its mean that a lot of pseudogenes contradict this claim (closer to gorila instead of chimp). so its not a prediction at all.

so how we can disprove the evolution theory if it can explain everything?

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I can only imagine that you don`t understand what is being said here. Just as there are thousands of ways to break a vase, there are an enormous number of potential mutations that can render a gene non-coding or a transcribed protein non-functional (indels are possible for every single base in the coding sequence, for example). Especially if a particular gene proves to be non-essential to survival in a number of independent lineages, it is hardly surprising that it would “break” or deteriorate in a number of different ways for many of them, since the conservative selection pressures that weed out errors would be fairly weak in each case. An enzyme that serves to produce vitamin C, for example, may independently become redundant in a number of species due to readily available alternate sources of vitamin C. To say “aha, look, all of these lineages that are not closely related have the same pseudogene, take that evolution!” becomes a very silly comment when it is obvious to all that this is a normal outcome within an evolutionary framework. It is merely a matter of the wide distribution of this gene combined with a frequently recurring basis for a reduction in conservative selection pressures. What would be surprising is if, for example, the very same frameshift mutation occurs in the same location within the same pseudogenes in genetically distant species, while this mutation is not found in closely related species. This would be a statistically unlikely outcome (though not impossible unless we see many instances of the same) in the evolutionary framework unless there is another mechanism that could account for it. In this case, it happens that there is such a mechanism, so the reasonable next step for a scientist would be to see if there is evidence of lgt in the genetic context. In short, you have failed to even consider whether the pseudogenes are the result of the same mutation, so your observation of the same pseudogenes in distant species is totally irrelevant, especially given that this is exactly what we might expect from this kind of gene (the GULO gene in this case). You have a few extra steps you need to take before this becomes even a vaguely interesting point that is worth pursuing.

At this point, incomplete lineage sorting has been referred to, explained, linked to, and illustrated for you so many times in this single string alone, that this paragraph is simply in excusable. If you don’t understand the response that you’ve already been given, that’s fine, but please say so. But what seems like a game of pretending, at this late stage, that you have not heard anything that explains this pattern can’t be taken seriously any longer. As it has been observed to you repeatedly, evolution simply does not predict that all of the genes will follow this pattern in closely related species. A more global observation is that many of your mistakes seem to relate to significant misunderstandings about or gross oversimplifications of what is actually predicted in evolutionary theory, and for some reason, you seem to resist strongly whenever it is pointed out that you have made a mistake about what is actually expected from the data and that not a single evolutionary biologist anticipates the pattern that you seem to think the data needs to have if evolution was a solid theory. Would it be right for me to think that you should know better based on your many interactions here?

Interesting confession. So you think the theory of evolution explains everything? A very generous gesture to your worldview nemesis, but I don’t think many of us would go that far. I think it’s fair to say that it explains many of the biological and paleontological patterns that we see, and where it doesn’t have anything to do with the pattern, I think we wouldn’t expect it to. More importantly, the standard scientific account about evolution and an ancient earth explains many of the patterns that YEC doesn’t even propose to explain, like the ordering of fossils and the consilience of independent dating methods. The usual strategy seems to be to find ways of dismissing the overall pattern by finding exceptions, since to admit that there is a pattern is to admit that there is something that needs to be explained and to tacitly admit that your hypothesis doesn’t do the job.

An alternate reading is that you were perhaps trying to convey the impression that evolution must be unscientific because it could not be falsified no matter what data is produced. In that case what you probably would have wanted to say is that evolution is unscientific because it can explain every hypothetical pattern that we might find in nature, not because it explains every pattern that we do find in nature (since this later outcome is hardly surprising – wherever evolution is expected to have explanatory power – if it is a successful theory). Since it is simply and obviously very untrue that evolution explains every hypothetical pattern that we might find in nature (there are an astronomical number of patterns that we might find that would be wholly inconsistent with evolution), this effort to make evolution seem unscientific is a dud.

I will go back to my vase breaking analogy; just as there are thousands of ways to break a vase, there are a limitless number of potential genomic, paleontological, and physiological (etc) patterns that would dramatically fail to fit with the theory of evolution or more specifically, with common descent. Every time that the theory is expected to explain a pattern of evidence but cannot, then either the source of this pattern is in need of serious investigation, or there is some other known factor that does explain it in a manner that is independent of the theory. Lgt is a good example of this, since it is not explained by common descent, but fits very well with other known mechanisms. In the past, you have appeared to be somewhat confused by this, somehow (I’m not sure I know how) coming to the conclusion that because something like lgt is explained by something other than common descent, it must therefore contradict common descent and falsify evolution. In the same way, a rock is not contradicting the theory of gravity because I’m lifting it up, it is simply rising because there is another, easily identified factor in play, and gravity does not need to panic about a potential loss of prestige.

I’ll wrap up by saying that this comment isn’t strictly for you. As I gather from your previous comments, and our previous discussions, you have a limited interest in letting arguments or new information change your views and would often rather redirect the discussion than acknowledge a correction, but I admire your persistence (and your uncanny ability to find and then unfortunately misunderstand scientific articles), and I tend to respond to you because I think that your comments are very good examples of typical creationist reasoning, which I find it endlessly fascinating to explore. For this reason, please excuse me in advance if I don’t end up following-up on any response that you might offer in this string!

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Thanks for the detailed explanations, @bren! What does the abbreviation “lgt” represent?

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Thanks Chris, it stands for lateral gene transfer (it has come up a lot in the discussions on this site, so it has often been shortened here).

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i already explained why this mean nothing. the main point is that a lot of genes are closer between gorila and human but not chimp. by the way- do you have any reference for the “prediction” of 15% similarity between gorila and human?

actually it can explain it. about the radiometric methods for example - do you think that a method that can be wrong in a factor of about 10^9 can be consider as a scientific method?

so what kind of fossil will disprove the evolution theory?

so how do explain this for example?:

http://www.biolbull.org/content/227/3/300.abstract

from the paper:

“The mechanism of gene transfer is of interest, but unknown”

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Actually, as far as I can tell, you have given no evidence of having read or examined anything anyone has cited regarding ILS. None. Zippos. Nada. Instead, you keep saying it can’t be true because of some other unrelated thing.

Please do the following so we can have a real discussion:

  1. Define incomplete lineage sorting
  2. Explain why biologists think that ILS explains the genetic lineage patterns among the great apes.
  3. Explain why ILS does not in fact explain the specific genetic data among great apes.

If you cannot do this, dcs, I will conclude that you are willfully refusing to read the sources that we are citing, even though you expect us to read the sources you cite. I have read all the sources you cited in this thread, dcs. Will you do the same for us?

If you do not, you will have demonstrated that you have no interest in a real discussion; you just want to shout. I hope this is not the case.

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sorry chris. you doesnt answer my questions to you either. so before we will continue i asked you 2 simple questions:

  1. if 2 species are much more similar from morphological prespective then the third one, therefore the third one cant be closer from dna prespective? (your claim).

2)how many disabling changes we are talking about? remmember that we talk only about identical changes (the same base\amino acid).

now to your questions: ils simply mean that some trait doesnt get fix in the population near speciation event, so a part of the population have trait a and other one trait b. the ending reslut (after fixation) is that some traits are shared between far species but not in the close ones.

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Your question does not even make grammatical sense, my dear friend dcs. I can’t answer a question which can’t be construed. But I think you asked the question in a more understandable form earlier:

And I answered:

I already stated that I agreed with bren’s answer to your question.

Since you don’t seem to remember bren’s explanation, I will repeat the most relevant part:

Thanks for providing a definition of ILS. But you have missed the most important question, the one that followed it:

Ball’s in your court.

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so if a fish is more similar to human then other fish from dna prpespective- then you will believe that fish are closer to human even if they look so different?

here is bren claim:

oh realy? again- even among pseudo-genes we find this pattern. again-in about 1/3 of them we will need to find this pattern.

because they odnt have any real other option. its after the fact explanation.

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Hi dcs,

I believe we are making progress!

This is a clearer formulation of the question, thanks.

Everything I’m about to say is coming from a non-biologist, so take it with a grain of salt or two or three. I have studied/practiced statistical methods and data science a fair amount, which is my best claim to qualification.

The answer depends on where the divergences have taken place. If the two fish species come from lineages that diverged before 390 mya or so, then the DNA proximity analysis could help determine which lineage is closer to land animals such as homo sapiens. If the divergence of the 2 fish species happened after the emergence of land animals, though, a DNA proximity analysis can’t help determine which one would be closer. In other words, we couldn’t use DNA similarity to determine which one is phylogenetically closer, because the branch happened too late in time.

That said, DNA similarity/divergence is a stochastic, probabilistic process. Therefore we would have to frame the analysis probabilistically (e.g., “within a 95% confidence interval, there’s a 55-90% chance the one is closer than the other”). And there’s no way a biologist could supply any meaningful numbers without having a well-defined and reasonably complete dataset. It may or may not be possible to do such an analysis today, because you would need to have to incorporate a lot more genomic data than the 3 species in question (homo sapiens and the 2 fish species).

If you are truly interested in a good answer to this question, you should ask a real expert like Steve Schaffner, and when he gives it, listen really carefully.

Please supply a specific pseudogene analysis so I can know what you’re talking about. In the absence of specific data, we can’t talk meaningfully about confidence intervals and probabilities.

Actually, Steve Schaffner’s genomic analysis is quite well-founded and is not post hoc. Here’s how it works:

  1. We have observed incomplete lineage sorting in contemporary populations. It’s an important and well-proven population genetics insight. [The example of my cousin Dan and my brothers][1] is but one example of data that illustrate the incomplete lineage sorting process.
  2. Since ILS is observed in population genetics today, we would expect that it also occurred in the past. That is, we would expect that if we perform thousands of cross-species genomic analyses, we would find many examples of ILS. I’m not sure exactly how many (that depends on the base rate, which I don’t know).
  3. The data from the ape/chimp/human analysis do, in fact, match the ILS scenario. ILS provides the best explanation for the data, so we infer that ILS happened.

Scientists are always making inferences, dcs. You may have heard recently about the discovery of gravitational waves. What really happened is that disturbances in the laser interferometer diffraction patterns in the Washington LIGO lab and the Louisiana LIGO lab matched very closely. These disturbances did not correspond to any observed terrestrial phenomena (earthquakes, heavy trucks, etc.). The fact that the disturbances measured at the 2 stations matched over a long period of time, but were only separated by 7 milliseconds, indicated that the source of the disturbances was moving at the speed of light. If someone were to argue that magical fairies acted in collusion at both stations to produce the coordinated diffraction pattern changes, I could not prove them wrong. I could only say that the scientific method prefers a natural explanation over a spiritual one.

Note that the scientific method does not exclude the role of spiritual explanations. It is quite possible to say that mathematically expressed laws of nature only have explanatory power because God has created the universe to be an orderly place. An atheist might disagree, and say that mathematically expressed laws of nature just exist, period. The fact that a Christian scientist prefers scientific explanations for paleontological data does not mean that she or he is applying post hoc explanations, or is somehow agreeing with the atheist about why the universe is an orderly place.

I hope you don’t mind the long discussion of the scientific process, dcs. This level of detail seemed to be appropriate in view of the question of whether the ILS explanation of primate genomic data is merely post hoc, or is actually good science. I can confidently say that it conforms to the practice of scientific inference over the past several centuries.
[1]: Vitellogenin and Common Ancestry: does BioLogos have egg on its face? - #11 by Chris_Falter

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why actually if the dna way is the best according to your standart?

again- if 15% of the genome is more similar between human and gorila, its also refer to the junk one.

if its true- why there is no source to the suppose 15% prediction before this finding?

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You are aware of the fact that “genomic data” refers to data about the genome, right? And of what does the genome consist, dcs?

Anyway, thinking like a statistician, I would imagine that establishing a base rate of DNA variance among fish (and among mammals) would be helpful in a statistical analysis. And a sample of 3 species would be far too small to measure variance. But again, I am not a biostatistician like Dr. Schaffner, so I would refer you to him if you really want an expert reply.

It seems like you’re asking about the GULO pseudogene among primates. If so, we’ve already had a very lengthy discussion on this topic. I am not interested in repeatedly repeating myself. It would be redundantly redundant.

I’m not sure exactly what you’re asking, my friend dcs. You have this habit of saying one or two words to express a complicated thought, and expecting that everyone will understand the thought. I say that to help you improve the quality of your writing.

But I’m going to assume that what you’re asking is this: “Why did no one predict the existence of an ILS pattern in the primate genomic data before it was discovered?” If that’s your question, I already gave an answer, two sentences after the part you quoted:

You seem to have stopped reading before you got to my analysis of why ILS is not a post hoc explanation for primate genomic data, but actually a very well-founded scientific inference. I invested a lot of my valuable time writing those several paragraphs for you, dcs. Did you find nothing of value there?

Honestly, my friend dcs, I’m seeing a pattern in your behavior. As a friend, I’m going to mention it to you so you can grow in God’s wisdom. Or if I am misunderstanding you, I hope you will forgive my misunderstanding and explain how the appearance I am perceiving is not the reality. We are part of a community of grace, after all.

What I’m observing is that as you read through what someone writes to you, you are thinking, “How can I immediately shoot down this comment?” When the very first possibility of refutation hits your mind, you dash off a response. Or you go to creation.com to find a source that you can quote, then you dash off your response.

And in so doing, you ignore the vast majority of what is being written to you. You don’t follow the links. You don’t pause and think, “What are some possible strengths of my friend’s analysis? Is there anything of value in what that person took the time to research, think about, and formulate in words for me?”

You want us to think carefully about what you write, dcs. You want us to follow your links, look carefully at the data you cite, interact with your argument, and answer your questions to the best of our ability.

I have in fact tried to do this with what you write, dcs. For example, when you mentioned in another thread that YEC and ID creationism would predict similar DNA for similar functionality, I agreed with you. When I misunderstood something you wrote, I acknowledged the mistake.

That’s what you want us to do for you, dcs. Will you do for us what you are asking us to do for you?

Rather than dismiss ILS as an arrogant, atheistic post hoc explanation for genomic data, would you think instead, “This is an interesting idea. I should explore how it might make sense. If I find some value in it, I should acknowledge that value and thank the person who brought it to my attention.” ??

When discussing whale evolution, will you stop saying, “Oh, I got 'em with that dolphin argument!” And instead say to yourself, “Dolphins are similar to whales, but they are different in some ways, too. My friend is spending a lot of time gathering specific evidence about whale anatomy so he can present it to me. I should see if those specific examples show something not seen in dolphin anatomy, and if so, I should consider what it means for the question we’re discussing.” ??

Will you do those things, dcs? Will you treat me as I am trying to treat you?

Thanks for listening.

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Thanks so much for that video link and the explanation. Very helpful:-)

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You are most welcome, @Professormom

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thanks for your kind comment chris.

true. but if you have 3 full genomes and you said that dna is the best way to conclude the phylogeny- its mean that 3 genomes its more then enough. so what is the problem?

no. its just a simple logic. if about 15% of the genome is colser between gorila and human then 15%

true. from what i know there is even one paper that predict this. what you refer is an after the fact argument. so can give any paper of this specific prediction in the gorila-chimp-human trio before this finding if its was a real prediction?.

ok my

why not chris? do you open to the possibility that dolphins and whales always been dolphins and whales?

friend chris. lets check it togheter. if the ils model doesnt true- what kind of evidence we should find to disprove this model?

of pseudogenes also closer between gorila and human.

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Hi dcs,

Thanks for your gracious and interesting reply.

Perhaps an underlying problem in our discussion is that I’ve been referring to statistical theory and methods to explain genomic data–but, unfortunately, much in the world of statistics is rather counterintuitive. It just is. The result is that someone who does not have a thorough grounding in the theory and methods of statistics is either going to have to just accept the statistical explanations on faith, or is going to need to put in some work to gain a deep enough understanding of statistics to figure out what’s being said. In every point of your most recent reply, your lack of background in statistics is quite apparent. There’s nothing wrong with that. No one expects every BioLogos commenter to have this background.

However, if I’m appealing to statistical theory to explain some data, but you don’t understand statistical theory–and you don’t want to accept statistical explanations by faith, so to speak–then of course it’s going to be hard for us to make progress.

So rather than my appealing repeatedly-yet-again-once-more to statistical theory and methods, I’m going to offer to help you understand biostatistics.

There is a series of 6 free courses in biostatistics available on edx.org. These courses are available from now until some point in September. If you enroll now and finish one course per month, you will end up with a solid background, and even ability, in biostatistics.

Video explaining the series: https://www.youtube.com/watch?v=nwFyIxc4AE0
First course, with enrollment link: https://www.edx.org/course/data-analysis-life-sciences-1-statistics-harvardx-ph525-1x

If you are willing to spend $49 per course, you can even acquire a verified certificate. How cool is that?

My offer to you is that I will spend up to 30 minutes per week in answering any questions you have about these courses, once you are enrolled in them. I have finished the first course, and am planning to resume the series in about a month, after I finish a couple of other data science objectives I’m working on now.

Are you interested?

Grace and peace,
Chris Falter

P.S. I am open to the possibility that whales and dolphins have no phylogenetic relationship. The genomic and paleontological evidence I’ve read point strongly to a relationship, but if there’s a simpler scientific inference to the evidence, I am willing to consider it.

However, I am not willing to discuss the issue until we have a common understanding of biostatistics. Our previous discussions have been unsuccessful because of a lack of this common background. So let’s walk before we run, ok?