Baranomes

[Mike Elphick]

It's good to see that not all young earth creationists accept the "adaptation by loss of information" dogma — that post-creation and post-Flood diversity of "created kinds" (baramins) is due entirely to degenerative mutations following man's Fall and God's subsequent Curse.

Of course you have to assume some sort of genetic front-loading to explain how pairs of "kinds" can walk off the Ark and start a process of hyper-evolution resulting in the vast number of species we see today. Nevertheless, Dr Jean Lightner is a creationists who finds it difficult to reconcile solely degenerative genetic changes as the mechanism for adaptation, and proposes a different model in which there are (or were) inbuilt mechanisms for specific adaptive genetic changes. She believes creationists need a "more robust" model to challenge universal common ancestry proposed by evolutionary biologists. Creationists need to have a clear understanding of the differences.

In an article "Comparative cytogenetics and chromosomal rearrangements", Lightner investigates chromosome arrangement (karyotypes] and the banding seen by chromosome painting methods.

Comparative cytogentics has been important in establishing that many mammals have undergone significant chromosomal rearrangements during their history. A diversity of karyotypes may occur within a genus or even a species. Given the considerable karyotypic diversity within some animal baramins (kinds), many of which were represented by only two animals on the Ark at the Flood, accounting for relatively rapid karyotype changes is a necessary part of the creation model. All rearrangements involve the repair of double stranded breaks. Additionally, many rearrangements are associated with alteration of heterochromatin, silencing of a centromere, and/or the formation of a new centromere. Because of the precision necessary to accomplish such changes while maintaining viability of the animal, it appears there are designed mechanisms in place to accomplish such rearrangements.

Lightner describes studies where a new in silico method of comparison, called electronic chromosome painting (E-painting), has been used to compare genomes of different mammalian species. These show that sections of chromosomes have undergone rearrangements, both within and between chromosomes. Some of these underlie inherited diseases whilst others are associated with karyotype diversification. These breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution.

Lightner argues that identification of patterns of intrabaraminic chromosomal diversity should help clarify what types of rearrangements are consistent with the creation model and believes that genomic comparisons, between or within baramins, should provide useful information on genomic structure. She tells us that creationists need to address the issue of genome organisation similarity between baramins at creation. The creation model will become more robust if this is better understood.

Dr Lightner seems to be suggesting that chromosomal rearrangements are observed to be non-random due to some inbuilt mechanism that generates new gene associations specifically for creating phenotypes that better suit organisms to different environments. However, she seems to be ignoring the fact that an evolutionary breakpoint is not just the result of some meiotic accident — it then has to make it through multiple viability tests at the gamete and zygote stages, and survive natural selection as an adult to procreate and then manage to spread its new chromosome arrangements throughout the population. Consequently, what we observe at the end of this process will not be random, even if there's a predisposition to breakage at certain loci.

But lightner doesn't stop there:- she tries to explain chromosomal rearrangements by introducing the crazy subject of baranomes and variation inducing genetic elements (VIGEs).

Baranomes

1. Baranomes are pluripotent, undifferentiated, uncommitted genomes. The origin of baranomes cannot be described in purely naturalistic terms.
   
2. Baranomes are frontloaded with three classes of genetic elements: I) redundant, 2) non-essential and 3) essential. Genetic redundancy is an intrinsic property of baranomes and serves both in robustness and rapid diversification.
   
3. The environment—habitat, habit or diet—often determines what part of the baranome is retained.
   
4. Essential DNA elements—although not completely static—are stable due to natural preservation ('natural selection').
   
5. Baranomes were designed to rapidly change arid adapt. That's why novel (adaptive) phenotypes always appear instantly.
   
6. Variation in baranomes is the result of genetic losses, duplications and translocations, and facilitated by frontloaded variation-inducing genetic elements (VIGEs). VIGEs are what mainstreamers call ERVs, UNEs, SINES, ALUs, transposons, etc. They induce variation from the frontloaded baranomes by swapping genetic information, facilitate duplications, disruption of (redundant) genes, position effects, etc. The major part of variation observed in nature is actively generated from inside.
   
7. Baranomes provide organisms with an urge to reproduce. Sexual reproduction preserves the baranome.

Evidence for the design of life: part 2—Baranomes by Peter Borger

How can someone (Peter Borger) with an M.Sc. in Biology and a Ph.D. in medicine and who's "an expert on the molecular biology of signal transduction and gene expression" write such unsupported nonsense?

If something can't be described in purely naturalist terms, then why bother trying?

In her article, Lightner states:-

A proper use of evidential arguments depends on a robust creation model which requires a more detailed understanding of genetic changes that have occurred during history.

Evidential arguments? But there IS no evidence!!! Just like "created kinds", baranomes are no more than wishful thinking and creationist invention. And despite what Lightner says, there is no evidence for facilitated or adaptive chromosomal rearrangements.

 

[Naraoia]

"pluripotent, undifferentiated, uncommitted"? For some reason I found seeing those words normally reserved for zygotes to be absurdly funny in this context. Likewise, making up a new name for mobile genetic elements. Trying to sound scientific without being mistaken for a "mainstreamer", eh?

There are a few ideas here that might actually be testable.

How much variation/adaptation can be attributed to mobile genetic elements? The baranome hypothesis states that "The major part of variation observed in nature is actively generated from inside." By "VIGEs", that is.

What did the ancestral genomes of each baramin look like (whenever someone actually determines what the baramins are)? The baranome hypothesis posits that "Genetic redundancy is an intrinsic property of baranomes". So did we lose redundancy as the "undifferentiated" genomes of animals went down different paths? Or has the level of redundancy increased? Remained unchanged?

Do novel adaptive phenotypes always appear instantly? (However, they'd do well to define "novel adaptive phenotype" and "instantly" in a way that a novel adaptive phenotype that doesn't appear instantly is at least a logical possibility!)

To what extent does the environment determine what part of the baranome is retained? This reminds me of a particular example of DNA repair mechanisms. IIRC, all placental mammals lack the photolyase pathway for repairing UV damage (which is a lot better than our remaining solution to the problem). Pretty much everyone else on the tree of life has it. And its absence from mammals has nothing to do with environment. (Well, not with our present environment. But I highly doubt the creation model posits a long nocturnal phase in human evolution...) How common are such occurrences, compared to cases when the presence or absence of a function is correlated with the organism's needs?

Of course, some of the above may not be able to distinguish between evolution and baranomes. For example, I don't think that genomic redundancy should always change in particular directions for evolution to be true. But testing if the predictions (such as they are - the whole thing seems like an attempt to cover all bases to me) of the baranome hypothesis actually describe real genome evolution could at least determine if the idea is wrong.

 

[SkyWriting]

It's good to see that not all young earth creationists accept the "adaptation by loss of information" dogma — that post-creation and post-Flood diversity of "created kinds" (baramins) is due entirely to degenerative mutations following man's Fall and God's subsequent Curse.

I've not heard that before. Checking the ICR website, I found no mention of the topic. Searching the web resulted in only 4 direct matches.

But biological circles seem to support the "dogma" to some degree. The article says that loss of information is not directed adaptation while mutations are. So the two are separate mechanisms for change.
BIOCHEMICAL ADAPTATION AND LOSS OF GENETIC CAPACITY IN HELMINTH PARASITES - FAIRBAIRN - 2008 - Biological Reviews - Wiley Online Library

 

[Mike Elphick]

It's good to see that not all young earth creationists accept the "adaptation by loss of information" dogma — that post-creation and post-Flood diversity of "created kinds" (baramins) is due entirely to degenerative mutations following man's Fall and God's subsequent Curse.

I've not heard that before. Checking the ICR website, I found no mention of the topic. Searching the web resulted in only 4 direct matches.

You wouldn't find much if you included the word "dogma" . Better to do a search with "new information", and you'd soon see that young earth creationists (YECists) refuse to accept that new (genetic) information can arise though naturalistic processes. Surely everyone participating in this forum knows that.

But let's start with a YECist statement of belief:-

4. The various original life forms (kinds), including mankind, were made by direct creative acts of God. The living descendants of any of the original kinds (apart from man) may represent more than one species today, reflecting the genetic potential within the original kind. Only limited biological changes (including mutational deterioration) have occurred naturally within each kind since Creation.
What we believe

And this from AiG:-

The biblical perspective on change within living things doesn’t require that new information be added to the genome as pond-scum-to-people evolution does. In fact, we expect to see the opposite (loss of genetic information) due to the curse in Genesis 3. Biblically, we would expect mutations to produce defects in the genome and would not expect mutations to be adding much, if any, new information.

Observations confirm that mutations overwhelmingly cause a loss of information, not a net gain, as evolution requires.

Mutations, when properly understood, are an excellent example of science confirming the Bible. When one sees the devastating effects of mutations, one can’t help but be reminded of the curse in Genesis 3. The accumulation of mutations from generation to generation is due to man’s sin. But those who have placed their faith in Christ, our Creator, look forward to a new heaven and earth where there will be no more pain, death, or disease.
Are Mutations Part of the “Engine” of Evolution?

And from CMI:-

An important aspect of the creationist model is often overlooked, but it is essential for a proper understanding of the issues. This aspect is the deterioration of a once-perfect creation. Creationists believe this because the Bible states that the world was created perfect (Gen. 1:31), and that death and deterioration came into the world because the first human couple sinned (Gen. 3:19, Rom. 5:12, 8:20–22, 1 Cor. 15:21–22, 26) ... From this premise of perfection followed by deterioration, it follows that mutations, as would be expected from copying errors, destroyed some of the original genetic information.
Deterioration from perfection

And again from CMI:-

Evolutionary concepts of descent with modification ultimately require the addition of new information over time in order to get from a dinosaur to a bird, for example. The biblical model does not require new information. In fact, the biblical model is confirmed by the fact that we see a loss of information as these species adapt to various environments. This is what we would expect as the world continues to deteriorate after the Fall. (See “Is Natural Selection the Same Thing as Evolution?”
Not So Common Descent(My bolding)

Therefore my statement that "adaptation by loss of information" is a YECist belief is true, though maybe not universal. Of course, I'm being somewhat facetious by using the word "dogma".

According to Peter Borger, this can be likened to a Swiss Army Knife:-

Genetic redundancy, dispensable genes and disintegrating genomes are scientific novelties revealed to us by modern biology ... The way to understand variation and speciation is through disintegration and rearrangement of primordial baranomes created with an excess of genetic elements. Baranomes initially contained all mechanisms required to quickly respond and adapt to changing environments. They provided organisms with the tools needed to invade many distinct niches, and were ideal for the swift colonization of all corners of the world. Baranomes were multifunctional genomes which can be compared to a Swiss army knife. A Swiss knife contains many functions which are not immediately necessary in a particular environment; but some of them are extremely handy in the mountains, others in the woods, still others are made for opening bottles and cans, or tools for making a fire. Depending on where you are, you may require different sets of functions ... The environment then determines what part of the non-essential genome is under constraint and it is only this part that will be conserved."

But biological circles seem to support the "dogma" to some degree. The article says that loss of information is not directed adaptation while mutations are. So the two are separate mechanisms for change.
BIOCHEMICAL ADAPTATION AND LOSS OF GENETIC CAPACITY IN HELMINTH PARASITES - FAIRBAIRN - 2008 - Biological Reviews - Wiley Online Library

I have difficulty understanding this 40-year old paper. I assume that the term "genetic capacity" defines the potential of an organism to perform certain tasks e.g. "the genetic capacity to overcome a host's defence mechanisms", or "the genetic capacity to metabolise certain nutrients". The term "adaptation" as used in the article, seems to be referring to the ability of individual organisms to respond, and not to evolutionary genetic adaptations. Without access to the pdf, I really don't know what the paper is telling us, perhaps you could explain?

 

[SkyWriting]

You wouldn't find much if you included the word "dogma" . Better to do a search with "new information", and you'd soon see that young earth creationists (YECists) refuse to accept that new (genetic) information can arise though naturalistic processes. ....<snip>

I searched with the idea you provided "adaptation by loss of information".

The issue is that there is no natural source for dna encoded language.
The use of symbolism is limited to intelligent sources.

A PubMed search for "new information" confirms my stand that genetic engineering by humans is needed to produce "new information".
new information - PubMed result

 

[Mike Elphick]

You wouldn't find much if you included the word "dogma" . Better to do a search with "new information", and you'd soon see that young earth creationists (YECists) refuse to accept that new (genetic) information can arise though naturalistic processes. Surely everyone participating in this forum knows that.

I searched with the idea you provided "adaptation by loss of information".

The issue is that there is no natural source for dna encoded language.

That's precisely what I just said, but the source of DNA is not the issue. The real issue is how the "kinds" managed to adapt post-Flood, after the severest genetic bottleneck possible, and then to generate the vast number of species we see today (and many others that have gone extinct).

What were the mechanisms? Was it simply a matter of genetic front-loading of the "kinds", with the progressive elimination of genetic information (adaptation through loss of information)? Or were there mechanisms in place that orchestrated and directed such information in pre-designed adaptive processes?

The OP is directed at the latter: first from a paper by Dr Lightner, who seems to be putting the case for a purpose-driven mechanism for chromosomal rearrangement, designed and directed towards adaptation: and second, from Peter Borger, who proposes the concept of baranomes (pluripotent, undifferentiated, uncommitted genomes) and VIGEs (frontloaded variation-inducing genetic elements), which direct variation in baranomes to create "novel adaptive phenotypes".

YECists go light-headed when they hear the word "code" and "language", as it applies to DNA, for this falls nicely into place with their concept of genetic "information" coming directly from the "mind of God" (and simultaneously refutes evolution at its very core). But it's one thing to have a belief and another have the evidence. Like created "kinds" (baramins), baranomes are no more than a creationists invention and lack any evidence, biblical or biological, for their existence — or previous existence.

 

[Blayz]

A PubMed search for "new information" confirms my stand that genetic engineering by humans is needed to produce "new information".
new information - PubMed result

Could you explain this further? the search you linked to has 118344 results, and on the first page of 20, only 1 concerns genetic engineering.

Doing a search for "new information genetic engineering" returns 1319 results, which is about 1% of all 118344.

 

[Naraoia]

A PubMed search for "new information" confirms my stand that genetic engineering by humans is needed to produce "new information".
new information - PubMed result

To find any relevant information (no pun intended) by PubMed search, you first have to know what to search for.

The thing is, "information" is not a word that is often used in this context. It's in fact quite hard to find what you are looking for with only one search term. That's because evolutionary biologists of all stripes are long past worrying whether "new information" (whatever that means) can originate naturally. We're more interested in investigating all the different ways in which it does. Here are a few terms in actual use in the literature that among them, cover some of the area:

- evolutionary innovation will give you all kinds of stuff, not just genetics
- gene duplication is pretty self-explanatory
- neofunctionalization is specifically the evolution of a new function in a gene (often following duplication)
- "functional evolution" (be sure to put this in quotes!) is not specifically about new stuff, of course, but new functions will be in there somewhere
- domain shuffling and exon shuffling might also give you some relevant results, since many new proteins are thought to originate via this mechanism (an important example)