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

Faith & Science Conversation
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I read the link and the abstract. You appear to have made an enormous leap which has no basis in either source.

Moreover, it appears you cherry-picked from the LiveScience article and overlooked (?) this very important statement:

"“So although most of the human genome is indeed closest to the
chimpanzee genome on average, a sizeable minority, 15 percent, is in
fact closer to the gorilla, and another 15 percent is where gorilla and
chimpanzee are closer.”

So it seems that the authors made the very opposite of your claim. They said “most of the human genome is indeed closest to the chimpanzee genome on average,” You appear to have zoomed in on the 15% (ignoring the 85%) and pretended that it “overturned” nested hierarchies when it was said, in fact, to have been a MINORITY (15%.)

In other words, the relationships found were VERY MUCH CONSISTENT with what one would expect in the nested hierarchies which point to common descent! Your argument leads the reader to suspect that either you don’t understand the kinds of evidence which Common Descent would produce, or you are assuming that your readers won’t understand what types of genomic evidence would be produced by such evolutionary processes and, therefore, you assume it would convince them that Common Descent has been “disproven.”

Yet, EVEN IF the very selective excerpt hadn’t been a blatant quote-mine, to make the fantastic leap amazes me, so I’ll quote it again:

Wow! I almost got whiplash from the huge G-forces of that explosive leap to your conclusion. (Pilots taking off from aircraft carriers have the advantage of pressure suits to prevent excessive pooling of blood in the legs. I had no such chance to prepare myself.) Similar logic would claim that because my campfire produces smoke which drifts upwards, Newton was wrong about gravity!

You have proven one thing for sure: Quote-mining is always risky. There’s always a chance that a reader will take the time to read the cited source.

Great links, however. Thank you for posting them. Very interesting.

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The other thing to mention is that based on evolution, we expect this effect with closely-related species - it’s called incomplete lineage sorting. If we didn’t observe it, it would be a problem for evolution. We expect that we will observe the most ILS with gorillas, and still less with orang-utans - and that is exactly what we observe. Notice that we don’t observe ILS with more distant species, say with non-primate mammals.

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Thank you! For the life of me, I couldn’t remember that term.

As happens so often, the very argument detractors think is a problem is in fact exactly what the Theory of Evolution predicts. Do ya think that might be why the theory is considered one of the very best attested in all of science? That’s my bet.

The creation science ministry leaders who spread these quote-mines have only vague ideas about how evolution works. So they actually think they’ve discovered some grand failure of analysis that all of the world’s scientists somehow failed to notice. Their followers deserve better.

When I was a young earth creationist, I managed to avoid jumping on the popular quote-mine bandwagon. But I was often guilty of thinking my scientific analysis was superior to that of the “godless evolutionists.” If any reader should wonder if it actually was…no. I wasn’t even close to understanding what I claimed to know something about. However, the humbling experience early in life was an important lesson to learn. Thankfully, being wrong now and then helps to sustain that lesson. So perhaps my background with Morris and Gish was a good preparation for life.

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no. my claim was about the fact that gorila and human shared a lot of bases that chimp doesnt have. so prof venema claim that we should see some mutations that are shared between humans and gorillas but not with chimpanzees if gorila is colser to human. and this is indeed what we found.

again not realy. if you will look at the tree that base on morphology you will get a different tree (gorila and human shared about 8 traits that chimp doesnt). if you will look at the fossil record you may find even more problems.

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Hi dcssss, you really might try reading up on incomplete lineage sorting as Dennis Venema mentioned. Apparently, one can calculate the degree where this would happen based on divergence times between lineages.

Perhaps you could offer a predictive model based on ID and YEC postulates that can be used to calculate the expected coalescence of genes in humans, chimps and gorillas.

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Hi dcscccc -

Generally, the most similar human being to me are my 3 brothers. However, for a few traits–height, body mass, competitive approach to sports and games, disposition toward engineering instead of art–my cousin Dan is closer to me. I think Dan is more similar on about 10% of my traits; but take that with a grain of salt, because I haven’t done a rigorous analysis. My brothers are more similar on the remaining traits.

It works the same way in the primate family. Overall, chimps are closer to humans than gorillas are; but on 15% of traits, gorillas are closer to homo sapiens. Since I’m sure you are curious about how this might be, I refer you to the previously mentioned concept of incomplete lineage sorting. At first glance it seems counterintuitive, but it’s one of the more important insights of population genetics. It even applies to allele distribution among humans, It is very well established science.

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Another example that might be of interest (although irrelevant to mammals) is the case of the respiratory systems of salamanders. Salamanders begin lung development, but it is aborted, and they end up expressing a gene for a gas channel in their skin. In other species it is a lung gene. The adult norm is breathing through their skin and an absence of lungs. I would expect that their genome has a bunch of lung pseudogenes, although this change in development may have occurred so long ago that the pseudogenes aren’t recognizable. I assume there is probably a salamander genome available. I have told Joel Duff of this, so Dennis can regard this as a competition of sorts on who looks into it first. :smile

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its actually a simple logic- if most of the genome is similar then the coding genes will be similar in the same way. its not a prediction at all but a common logic.

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but what about the overall from morphological prespective? did you know that gorila and orangutan are more similar to human then chimp? so who is closer to who and what is your correct way to know this?

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DNA similarity is definitely the best way to go. For example, if a woman wants to prove paternity in a lawsuit against a deadbeat dad, she obtains a forensic DNA analysis of the man and the child. She doesn’t say that the man’s nose looks similar to the child’s. Well, she might! But it wouldn’t be very strong evidence. DNA is much stronger evidence.

Similarly, the best evidence for the phylogenetic proximity of various primates is the overall similarity of their DNA. Since the genome of chimpanzees is (overall) closer to homo sapiens’ than gorillas’ or orangutans’, it makes sense to conclude that chimps are closer to us phylogenetically.

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You are correct, my friend dcscccc–similarity of coding DNA for similar functionality would be a prediction of both YEC creationists and evolutionary creationists (ECs).

YECs and ECs would make different predictions for non-coding DNA such as pseudogenes, however. From the YEC perspective, there’s no reason to predict similarities of non-functional DNA. From the EC perspective, however, the closer the ancestry, the more similar the non-coding DNA should be.

The difference in these 2 predictions should prove very helpful in sorting out which school of creationism is more scientifically accurate.

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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.

im not so sure. the gulo pseudogene (and a lot other) for example get lost in several species by convergent loss. so even the creation model can fit with the non-functional DNA.

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its actually a simple logic- if most of the genome is similar then the coding genes will be similar in the same way. its not a prediction at all but a common logic.

I’m not sure what you’re addressing. How does one get from a non-evolutionary model to produce positive predictions about genetic similarity between separately created species? What additional hypotheses are you including to determine that human sequences should appear more similar to gorillas 15% of the time, vs. similarities with chimps? You seem to suggest gross morphology might explain it but you’d have to include yet more hypotheses of how tightly coupled DNA sequences must be to overall morphologies or phenotypes. What are these assumptions and have they been demonstrated? I know one can find conserved portions of some sequences that have a huge effect on viability, but from what we know from genetic engineering today, it’s hard to make the case that this would extend to include 98%+ of the genome.

Basically, special creation provides little basis for distinguishing any particular pattern of similarity. Perhaps someone like Todd C. Wood will achieve some success in the future but right now, he has no clue how to begin. The additional hypotheses necessary to ground the notion are just not there (see also Elliott Sober’s explanation of the need for ‘auxiliary hypotheses’ in his book, Philosophy of Biology). Currently, common descent and contemporary understanding of genetics provide much better explanations. You might wish to google ‘incomplete lineage sorting’, as has been suggested earlier.

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hey argon. again- its not a prediction of evolution either. so i doesnt see any problem here. actually: some fish are different in the non-coding region but colser in the coding one (to human) then other fish. so in this case you will agree that evolution is wrong?

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dscccc, Two things:

  1. Different tools are best for different scales. Some parts of the genome are better for comparison than others. The signal and applicability for completely neutral sequences will degrade in hundreds of thousands to millions of years. A small number of sites has relatively higher noise-to-signal ratio than thousands of sites or larger features (like gene order).

  2. Divergence is a stochastic process. One does not expect perfect concordance in every case. However, one can model such processes with statistics to derive expectation figures. That is why, for example, we can understand the relative distribution of ‘more similar’ sequences between the great apes. Dennis Alexander discussed this previously in at least two posts:
    Evolution Basics: Incomplete Lineage Sorting and Ancestral Population Sizes
    Coalescence, Incomplete Lineage Sorting, and Great Ape Ancestral Population Sizes

Look, the observation that helium balloons fall upward from Earth’s surface is no more a contradiction or unexpected prediction for gravity than deviations from a perfect correlation between DNA sequences affected by stochastic processes. Over the years, I noticed that many YECs keep looking for some ‘magic’ bullet’ or perfect argument when what they really need is a better explanation for the preponderance of observations already collected. Todd Wood is at least honest about the task before him in trying to establish some sort of foundation where numbers and assessments can be made. Simple ‘negation’ in lieu of actual argument does not work (pace: Monty Python - linked here).

(edit 16-Feb to fix link. Thanks for the catch, Chris_Falter)

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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?