Scrambled Eggs and Ham?


(Phil) #1

AiG is a little testy and seems to have a little attitude with this critique. We have discussed a previous article about the topic before, but wonder if anyone has any comments regarding this one? I confess that my knowledge of genetics is enough to understand the language, but not enough to judge the validity of much of what is going on here.


Comparative genomics software
#2

It would appear that AiG didn’t read the primary paper too closely, which can be found here.

If you click on Figure 2 and go to the caption, you find these conclusions:

“Alignment of flanking genes confirms the synteny of the aligned regions. The combined alignments of VIT1 coding sequences showed significantly higher alignment scores than the genomic background (introns and intergenic regions) in the chain, as assessed by a Mann-Whitney U test (p < 0.05). Thus, we can statistically exclude that detected VIT1 remnants from humans represent spurious sequence matches.”

Let’s unpack this for a more general audience. Genes are stretches of DNA that are transcribed into RNA. That RNA is chopped up into chunks called exons and introns. The introns get tossed out and the exons are stitched together to create the functional messenger RNA that is then used as a template for making the vitellogenin protein.

So why does this matter? When you compare the genomes of divergent species you will find that the DNA associated with the exons, the chunks of DNA that eventually result in proteins, share more bases with the same exons in other species. The introns tend to have more differences than the exons. This is an expected outcome of evolution called conservation. This is caused by negative selection against deleterious mutations in the functional part of genes, and it results in fewer changes occurring in exons than in the introns which mostly lack function.

If humans (or other placental mammals) do have an egg laying ancestor then that egg laying ancestor should already have had conserved sequence in the exons of the vitellogenin gene. Even if vitellogenin became a pseudogene, that signal of conservation should stick around for a long time because it will take a lot of mutations to make that conservation of sequence blend into the genomic background. Think of it as trying to change a picture one pixel at a time. It will take a lot of changes before the image is degraded to the point that it looks like random noise.

What the authors of the paper found is that the regions corresponding to the exons of the vit1 gene in chickens shared more bases with the human genome than the introns and regions between genes. The evidence isn’t about a set percentage of shared bases. Rather, it is about the difference in sequence conservation between the exons of the vitellogenin gene and the introns/intergenic regions that surround them.

This is the data that AiG needs to address. Why is there more conserved sequence in the regions of the vit1 exons than in the introns and intergenic regions? How does AiG explain this? Evolution explains this perfectly, but I don’t see how creationism can. In fact, creationism can’t even explain why the sequence divergence of exons and introns is different, and why that divergence correlates to evolutionary distance. The vit1 gene is hardly the only gene that poses a problem for creationism. Each and every gene conserved across many divergent vertebrate species poses a very strong challenge to creationism due to the pattern of sequence conservation between exons and introns, and this is also very strong evidence for evolution.


#3

The following webpage is a bit of a mess and I don’t know if my formatting will carry over, but I thought I would give it a try.

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr20%3A46010454-46014434&hgsid=603187401_x92qOXuJdwxltFiNsMQy0RM9AVrm

This is a comparison of the human MMP9 gene to the same conserved gene in many other species. The line with boxes at the top is the MMP9 gene, and the boxes represent the exons for the gene. If you look below the representation of the human gene you will see one line with tall blue spikes. Those are the regions of conservation across 100 vertebrate species. The blue spikes represent areas where the genomes share DNA. As you can see, those areas of conservation line up with the exons. This is what we would expect to see if evolution is true, and it is what we do see when you line up the egg yolk gene in the chicken genome with the same region in the human genome.


#4

I can’t read an AIG article for very long without having high blood pressure problems—yet I even click on their links at times, where I read some of the article which precedes the one which JPM linked above. There I found this statement by Dr. Jeanson:

“Unlike human languages, scientists do not become proficient in the language of DNA by studying textbooks and databases of vocabularies. Instead, they learn the language by doing experiments.”

Tell me if I’m wrong. The above sounds like a silly claim to me. Yes, experiments are important, but it is my understanding that scientists can learn a lot from software analysis of DNA databases which already exist—and by consolidating/comparing results from various experiments and looking for patterns in the DNA sequences, especially when comparing genomes of various species. Isn’t he setting up a false dichotomy?

I admit to being biased when reading AIG materials—because I am so accustomed to finding bizarre claims and illogical reasoning. Are Jeanson’s often somewhat snarky articles (where “evolutionists” are always the bad guys) as mistaken as it appears to me?


(Ray Bailey) #5

I’m no expert, but I read their article carefully, looking at the language. I did this before reading @T_aquaticus posts. In it I found many false arguments in both the explanation of what BioLogos is supposedly saying and in the response.

This statement is pejorative in “Assuming Facts not in Evidence”. The author is assuming that the Dr. Venema has assumed such a thing.

This same statement can also be a “Genetic Fallacy Argument” (pun intended) in that he automatically assumes anything Dr. Venema says is tainted and unworthy of serious reply. He continues by then “piling on” with a highly simplistic but “pleasing to his audience” metaphor that leads to further impugning the motive of Dr. Venema and the study.

The rest of the article is full of graphics and wording that attack Dr. Venema as being incompetent (misreading the data, mislabeling the data, misrepresenting the data), combined with ad-hominem attacks on his sincerity (he didn’t provide the all important percentages that we demand, therefore he is a bad person, as well as by extension the group (BioLogos) that he represents.

That is enough for me. There is so much complex scientific data that requires intense and technical knowledge, mixed with inappropriate and fallacious arguments that it appears to me, a novice in this arena, that the supposed “Egg on BioLogo’s” face seems instead to be “Green Eggs And Hamming it Up” (pun for Ken Hamm) for Dr. Jeanson’s face.

Ray :sunglasses:


(Larry Bunce) #6

Even with my limited knowledge of genetics, I can see problems with the AiG article. The position of words in a sentence bears little on the meaning of a statement, so the analogy used to belittle Dr. Venema’s claim is faulty. It has been well-established that specific genes occupy similar places in multiple genomes. No mention is made of the expected match to be found in a gene after as many millions of years as separate humans and chickens from our common ancestor. I would guess that 20% over a random match is meaningful.
Placental mammals evolved from egg-laying mammals, not chickens, so the claim of chicken-to-man evolution is false, designed to make evolutionary claims sound ridiculous to creationists.
All in a day’s work for AiG. (Am I making an ad-Haminem attack on AiG?)


#7

What?? I must be misunderstanding your meaning. Word order in English is enormously important. For example, “The dog bit the man.” has a hugely different meaning from “The man bit the dog.” And even though a highly inflected language like New Testament Greek is too often characterized as “The word order in Greek is not rigid because word inflections do much of the work.”, randomly reordering a Koine Greek sentence of more than a few words produces a bizarre confusion that is hardly recognizable, although the inflections will go a long way to get the general idea across even after the scrambling. Even so, noun phrases in Greek, for example, don’t always hold up if the order is scrambled, especially if the article+adjective+noun becomes noun+adjective+article. (And some reorderings can cause the adjective to start functioning like a noun!)

By the way, my favorite example of the importance of word order in English is a rule that every native speaker knows but rarely thinks about. (It gives non-native speakers absolute fits!) When we use multiple adjectives in series, they always have to be in this order based on their function/category:

opinion-size-age-shape-color-origin-material-purpose + Noun.

Thus, we speak of “little green men” coming from the planet Mars and never “green little men.” And if we try to cover all of the categories of adjectives in one example, how about something like:

My favorite little old barrel-shaped black Austrian plastic guard dog sits on my front porch.

But randomly changing the order sounds not at all right to native speakers of English:

My barrel-shaped Austrian plastic old black guard favorite dog sits on my front porch.

It not only sounds extremely awkward, it creates a very different meaning! Yes, word order is very important in English.

I certainly agree with you that Jeanson’s article is faulty!


(Ray Bailey) #8

OSASCOMP always works!

@Socratic.Fanatic Thanks for the excellent tutorial! You bungled me to saved reply from a Larry (You saved me from bungling a reply to Larry!)

[quote=“Larry_Bunce, post:6, topic:36456”]
All in a day’s work for AiG. (Am I making an ad-Haminem attack on AiG?)
[/quote] I loved your response, with the exception of the sentence on English, :grin: so I gave you a “like”.

Ray


#9

Correct. This would mean that if we went back in time and compared the vitellogenin genes between those egg laying mammal ancestors and modern bird ancestors we would find more conserved sequence in the exons of that gene than in the introns. Even after the vitellogenin gene became a pseudogene in placental mammals, it would continue to carry that signal of sequence conservation until neutral mutations reduce it to background noise. What the chicken-human comparison demonstrates is that we still have sequence conservation in exons as compared to introns which we inherited from our egg laying mammalian ancestors.


(Larry Bunce) #10

Thanks for the responses to my post. Bill kills Bob is not the same as Bob kills Bill. The word order I was thinking about was when comparing two statements where one may have derived from the other, the Nth word in one may be unrelated to the Nth word of the other. This is especially true when the statements are in different languages.
In genomes, individual genes often occupy the same location in multiple species, or fit into a common sequence of genes.


(Ray Bailey) #11

Larry,
I should have read your context more tightly. Being the Language guy, I entirely forgot that you were speaking using the language of “word order” like in genetics. Hah! So much for trying to understand each other while divided by a common language!

Let alone determine what Genesis means over 6,000 years (or whenever) from the verbal stories to Proto-Hebrew, to Moses, to the Hebrew Priests, to the post-exilic editors, to the LXX, to the Latin, through the monks, to the reformation, to KJV English, to Modern English! Sounds like reading a DNA string or proteins!

Ray :sunglasses:


(Kendal Howard) #12

AIG always has made me cringe a little with their wording. Even when I was YEC. The articles always are full of attacks and assumptions. Always quick to declare the apostasy or biblical illiteracy of everyone who disagreed with them. The title “does biologist have even more egg on it’s face” is sooooo unnecessary. It’s annoying. It’s provoking. Rant over lol


(Phil) #13

The article they have on the website today is even more venomous and misleading. They must be really frightened to stoop to such depths of character attacks and ad hominem arguments, along with trying to confuse the issue with technical arguments presented to a lay audience to impress their readers.

It would be nice if they had a mechanism for comments and corrections, but unfortunately, do not. I occasional look at their facebook page, but the comment section is edited and not really appropriate for serious discussions due to the amount of random comments.


#14

AiG still doesn’t get it. Here is a portion of their previous work as quoted in the new webpage:

“When the human vtg pseudogene fragment [the 150 nucleotide fragment] was aligned using very liberal gapping parameters (see Materials and Methods) to the chicken genomic sequence, sequence identity was only 62%. Genomic DNA surrounding this fragment was sequentially increased three-fold in size (symmetrically) and each fragment aligned up to 36,450 bases of human genomic DNA. Sequence identity dropped as the fragment size increased, eventually leveling off to about 39% identity for a region of 36,450 bases.”

Well, duh. That’s what we would expect to see with a human vitellogenin pseudogene that was inherited from an egg laying ancestor when compared to the homologous chicken gene. You should see much less shared identity once you include large introns and flanking regions. The evidence is the higher conservation in the smaller exons which AiG tries to cover up by mixing them in with the introns.

It would appear that AiG still doesn’t understand the basic evidence and how it is analyzed.


(Joel Duff) #15

I’m not sure how to interpret this but as a close observer of the AiG webpage and associated social media outlets I have noticed a trend in their marketing of information. Nathanial Jeanson receives remarkably little coverage at AiG. This series of 3 articles attacking BioLogos continues that trend. All three articles have appeared on the AiG front page because everything published goes there but then almost every article is then pushed to social media within 24 hours. AiG, Ark Encounter, Ken Ham all have FB and Twitter accounts and I see the article usually appear on multiple of these accounts. So far none of Jeanson’s three article have been pushed out to social media outlets. Jeanson has put them on his FB page but he has fewer followers than possible anyone at AiG. They don’t seem interested in promoting anything he writes and this isn’t’ the first time.
Its as if, they just want to be able to say they have a Harvard PhD on staff and only if asked point to things he has written. If they really thought this was great stuff and was really sticking it to BioLogos wouldn’t Ken Ham be tweeting this article and commenting on it? It feels to me as if they want to show up BioLogos but that they also don’t want to bring too much attention to Venema’s book. I could be wrong, and maybe they will start up a big media campaign with Jeanson front-and-center soon but I’ve seen Jeansons’ work ignored time and time again by his own colleagues. BTW, Jeanson has a book coming out this fall entitled: Replacing Darwin: The NEW origin of species. I expect this will be the synthesis of AiGs view of hyper-speciation after a global flood. I will be watching the response to this very carefully.


(Jay Johnson) #16

Is it because almost everything he has to say – outside of the personal attacks and venom, which everyone can understand – is far too technical for the average person, and Jeanson doesn’t have the communication skills to make himself either understandable or relevant to the AiG audience? In other words, he’s mostly ignored because he doesn’t resonate with the audience. As you say, AiG wants a (in)credible response to @DennisVenema for anyone who goes looking for it on their website, but there’s no point in promoting Jeanson because no one will make it past the first few paragraphs.

Replacing Darwin: The NEW Origin of Species. I’m sure that will put Jeanson in the history books. People 100 years from now will be debating Jeansonsim vs. Darwinism … or not. Lol


(Joel Duff) #17

He is hard to read and he is difficult to respond to because many times I can’t even figure out what he is saying and so its hard to replicate what he has done. I feel the same with with Tomkins who doesn’t provide enough of his materials and methods to understand his work.
I think you are right. The bottom line is that AiG just wants a response so that they have a reference to point to and act as if they have provided an answer to their critics.


#18

Those articles may be over the head of the general AiG readership and the general public. I would suspect that only the science nerds are really diving into those articles.

[I see that others have come to the same conclusion]


(Jay Johnson) #19

If he and Tomkins made themselves crystal clear, they would be too easy to refute. It’s easier to make leaps in logic when no one can follow the logic, anyway.


(Jon) #20

He’s not even wrong.