Abiogenesis refers to a theory about the origin of life (sometimes seen abbreviated as OOL) that says living organisms arose from non-living matter through natural processes. Scientists involved in origin of life research propose hypotheses about possible mechanisms by which non-living entities could have theoretically transitioned to living entities in a series of events. However, possible mechanisms for abiogenesis are not currently very well understood. Research into abiogenesis draws on multiple disciplines including molecular biology, paleontology, biophysics, biochemistry, and oceanography. Many Christians mistakenly conclude that abiogenesis is part of the theory of evolution, but the theory of evolution only models how life is related to other life through common descent. Christian scientists have different perspectives on abiogenesis. Some think that eventually scientists will be able to describe how life arose from natural processes, but do not think that would diminish God’s role as the creator of life any more than evolution diminishes God’s role as the creator of the diversity of life. Others think that some kind of supernatural activity that will never be understood by science was required to initiate life. (See god of the gaps argument.)
I was spending most of my glossary-reading time admiring your liberal arts “ignorance”. I’m just hoping to help maybe plug some holes. And in that pursuit …
How about …
“Geocentric” (or ‘-ism’)
“Geostationary”
“Heliocentric” (or ‘-ism’)
And as more tools in the arsenal of science …
“repeatability” (or “reproducible”)
“prediction” (could speak as to how this need not be chronological prediction - although it’s always sexier when it happens that way, but how a theory can ‘predict’ already existing data.)
[Oh – and how can we forget: “Model” ]
Good thoughts. Added to my candidate pile. I was hoping to be DONE in the next two weeks, but the stupid things multiply like bunnies and can get pretty time consuming, considering I often have to learn stuff myself before I can explain it.
I have done some further reading and I think I may indeed be confused. (@DennisVenema do you have any input to set me straight here?)
I wrote an entry for gene duplication at the request of one of the reviewers (but it has not been checked).
Gene duplication happens when an extra copy of a gene is made in an organism’s genome. Gene duplications provide a source of new genetic material for mutation, genetic drift, and natural selection to act on, making it an important mechanism for creating genetic novelty in organisms. Many new gene functions have evolved through gene duplication. For example, in an ancestor of apes and some monkeys, a gene that codes for one of the two pigments found in most mammal eyes was duplicated. Mutations in one copy of this duplicate gene resulted in a group of light-sensitive proteins in the retina that could detect a different spectrum of light. Mammals with this gene duplication gained trichromatic color vision, while other mammal species such as dogs and cats only see greens and blues.
So, are pseudogenes the result of this kind of duplication event, or are they a result of replication errors that render the gene non-functional? Or are both possibilities? Do duplicate genes occur together in the genome? If they do, couldn’t you still say they occur at a homologous location as the original gene that was duplicated?
Your first mis-step was to open it up to us all here. 
Are you talking about unitary pseudogenes or processed pseudogenes?
Whichever one is cuter?
Here is my short explanation that is evidently lacking:
Pseudogene refers to a sequence of inherited DNA that resembles a functional gene, but over the course of evolution, it has mutated into an inactive form that is unable to code for proteins. Pseudogenes that originate by duplication are homologous to an ancestral gene. That is to say, they are found in corresponding places in the genomes of the two related organisms. The presence of the same pseudogenes in two species is strong evidence for common descent. The patterns of shared mutations in pseudogenes form nested hierarchies and show how closely species are related to one another.
Is this gene duplication? Or errors in gene replication?
Kinda a word salad that seems to be talking about both unitary and processed pseudogenes, but not well about either. I can try take a stab at it tonight if no one else does by then. Maybe ask Kathryn? Or Sarah?
Please have at it.
I should have stipulated that you need to provide a draft entry for every word you suggest. Then maybe I could have gotten some free labor instead of just more work. 
It might be good to add references (in the abiogenesis entry) to some of the terms used for newer developments in abiogenesis, such as pre-biotic evolution and metabolism first theories, even if it is just a (see) parenthetical at the end. The point of both is that the biology old guard like Dawkins, equating life with self-replicating molecules is falling a bit by the wayside, with an understanding that prokaryotic cells and RNA/DNA are likely to be the product of an evolution-like process themselves. Another important point is that abiogenesis isn’t just an off-hand suggestion but an ongoing area of active research.
Is this related to RNA world?
Sure. That is the hypothesis is that RNA is a holdover from a previous stage in the pre-biotic development which eventually produced DNA.
on falsifiability
The point of the objections might be that mathematical and speculative enterprises like string theory is an important part of the scientific process even if none of it has been legitimized by experimental confirmation. But it doesn’t change the fact that string theory cannot be accepted as scientific fact until we do have experimental confirmation.
So falsifiability and the scientific method remains a standard in the process of something becoming scientific fact but NOT a requirement for something to be considered part of a scientific inquiry.
“Recently, some scientists in highly theoretical fields have questioned whether falsifiability is a criterion for investigation to qualify as scientific inquiry, claiming that some areas of science may have reached the limits of what is empirically testable.”
Would that clarify it sufficiently? As I understand it they are complaining about the contention that they have wandered out of science into metaphysics and philosophy.
I would prefer something more this this:
Recently, some scientists in highly theoretical fields have questioned whether falsifiability is a criterion for investigation to qualify as scientific inquiry, even if it remains a necessity before something can be accepted as a scientific fact.
The point is that falsifiability remains an important criterion even if it not quite as originally explained. This is still a radical alteration because most scientists don’t want to get lost in endless speculation. In some sense what keeps things like string theory at least somewhat grounded is the mathematics. Mathematical discoveries in these areas turn out to be useful even when the theories themselves remain nothing but speculation.
Eisegesis refers to interpreting a text in a way that introduces one’s own presuppositions and biases. Some people refer to it as “reading into” the text. When people come to the Bible with a different cognitive environment, a different culture, and a different worldview than the original audience, it is easy to interpret a meaning that was not intended by the original author. Another form of eisegesis is taking a verse or passage out of the context in which it was meant to be understood and using it in a different context that twists the meaning. This is sometimes referred to as proof-texting. (See exegesis, hermeneutics.)
Hi Christy,
I’ll try to respond to the phylogenetics if nobody else has when I have some time, but as I started this pseudogene fire, let me help put it out!
So as you stated, a pseudogene is considered a nonfunctional gene, that either is no longer transcribed or it is transcribed but cellular mechanisms halt the translation process due to the presence of inactivating mutations (specifically stop codons).
Processed pseudogenes, which are perhaps less interesting for the evolution / creationism / ID discussion (others may disagree! I’d be happy to be wrong), arise from mRNAs being reverse-transcribed back into the genome. So imagine a gene gets transcribed, has the introns removed, forming a mature mRNA, and then that RNA product is reverse transcribed into DNA that is inserted into the genome. This “gene” doesn’t have introns or the correct regulatory elements (e.g., promoter) so is not transcribed, translated, etc. and eventually mutates to be less and less similar to the original gene.
Unitary pseudogenes are pseudogenes derived from a formally functional gene. For example, ENAM encodes a protein that is involved in seeding hydroxyapatite crystals to form enamel in toothed vertebrates. However, multiple lineages of vertebrates have lost teeth and/or enamel, such as anteaters, baleen whales, birds and turtles. The ENAM gene, however, is still present in the genomes of these species, but has become a pseudogene, either via selection against the retention of the gene or relaxed selection, in which the retention of the gene has been neutral and it has slowly decayed. Essentially, these species no longer have teeth and/or enamel, but the presence of the pseudogene points to a history where their ancestors once did (I liken them to genomic fossils).
The connection to gene duplication is this: since gene duplication leads to the generation of two different descendant genes from a single ancestral gene, it is generally thought to lead to one of the four scenarios below, which includes the formation of pseudogenes:
-
Both genes are retained due to an advantage to have additional protein product present. Think, for instance, of duplicating a gene involved in detoxification; having additional protein may help to detoxify the body more rapidly.
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Both genes are retained, with one descendant gene retaining the ancestral function, and the second mutating such that it leads to a gene with a novel function (neofunctionalization).
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Both genes are retained, but both mutate: one descendant gene retains part of the ancestral function, and the second retains another part of the ancestral function. For example, if the ancestral gene product digested, say, chitin and cellulose, the gene duplication descendants (paralogs) may diverge into chitin-digestion only and cellulose-digestion only enzymes. This is known as subfunctionalization. (for the record, 2 and 3 could be thought of as two different ends of a spectrum)
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Finally, the relevant part for this topic: if only one descendant gene is adaptive to retain, the other paralog can simply accumulate mutations until it becomes a pseudogene.
Let me know if you need me to clarify anything!
In case it isn’t too late then … (won’t hurt my feelings if you discard all of this or have already done it yourself. You said ‘drafty’ and well … that it is.) [now I see, I misread ‘draft’ as ‘drafty’ and I got excited … taking that quite literally! 
]
Geocentrism: is the belief that the cosmos is geocentric; that is, all the stars, sun, moon, and planets all revolve around the earth. For most of recorded human history, this was the prevailing understanding, and the simplest one to explain the apparent daily rotation of all these things overhead in our day-night cycle. The belief also entailed a geostationary earth - attributing all motion to celestial bodies, and no motion whatsoever to the earth. This cosmology dominated despite early occasional challenges - the main contender eventually being heliocentrism, but geocentrism remained the popular view through much of the 17th and even into the 18th century.
Heliocentrism: the belief that the cosmos (including the earth) all revolves around the sun. Though the heliocentric idea existed as early as Aristarchus (310-230 BCE), it was not until Copernicus, much later, that the idea was formally published, and even then - did not cause much stir until Galileo (later yet) aggressively promoted it. While Galileo is now rightly remembered as an important Copernican promoter, it was really the work of Johannes Kepler and Isaac Newton that finally led to the demise of the old geocentric cosmology. Some nagging scientific questions and evidences (such as the apparent lack of stellar parallax) would have to wait till much later, and much more refined instrumentation to be resolved. Christians up to that point (e.g. Cardinal Bellarmine) saw Scriptures as supporting geocentric and geostationary cosmology, and they saw no reason to challenge this long-standing view, as the science at the time actually weighed heavily against it. Galileo challenged this use of scriptures, insisting that questions of astronomy were not the domain or focus of scriptures. He famously wrote: “the Bible teaches us how to go to heaven, not how the heavens go.”
Geostationary historically referred to the belief in an unmoving, and immovable earth, though the same adjective has now been re-purposed to refer to a separate concept: ‘geosynchronous orbit’. But the older usage went along with a geocentric cosmology and enjoyed the support of all observational science of the day. There was no observable stellar parallax they could detect at the time, because the universe is much larger than they imagined. There were no consistent high winds as would be expected if the earth were moving through the air around the sun. Birds would be unable to keep up with an earth moving that fast, and finally: Scriptures themselves make clear reference to an unmoving earth. So in that time, there simply was no compelling reason to think the earth moves; at least not until Copernicus, Galileo, and finally Newton ushered in the centuries-long Copernican Revolution, and with the laws of motion showed that the earth can and does move rapidly!
[the above edited for additional clarity and/or brevity, and two more definitions added below.]
A model in the scientific sense is a useful representation of a more complex system. Models are valued for their explanatory and predictive power, and they are adjusted, overhauled, or even entirely replaced by better models according to their ability to explain, or predict the most data. A very current example of modeling is in the field of climate change. It is important to realize that a model is not expected to be a perfect representation of reality, but instead simplifies a complex system enough so that it is computationally accessible, and yet takes enough into account to still be predictively successful. It has been famously observed: “All models are wrong, but some are useful”.
Prediction commonly refers to the successful anticipation of future events. And while this is an exciting part of the success of science (e.g. Haley’s successful prediction for when the comet, now bearing his name, would return), it is nonetheless not the only way prediction is used. A theory or model also must successfully predict (i.e. explain, or successfully take into account) the already existing body of data at hand. Its ability to do this is seen to be its power or success in science. It is challenged, then, only if a competing model or theory does a better job, explaining even more than its predecessor.
And, returning to my hobby horse, the slippery word “biblical”. This is usually deployed as if about to give thoughtful exegesis, but very often (dare I say ‘usually’?) is opinion-based eisegesis.