There's one sub-category of pseudogenes that deserves mentioning. It's called "polymorphic pseudogenes." These are pseudogenes that have not become fixed in the genome so they exist as an allele along with the functional gene at the same locus. Some defective genes might be detrimental, representing loss-of-function alleles that compromise the survival of the organism. Lots of genes for genetic diseases fall into this category. That's not what we mean by polymorphism. The term usually applies to alleles that have reached substantial frequency in the population so that there's good reason to believe that all alleles are about equal with respect to natural selection.
Polymorphic pseudogenes can be examples of pseudogenes that are caught in the act of replacing the functional gene. This indicates that the functional gene is not under strong selection. For example, a newly formed processed pseudogene can be polymorphic at the insertion site and newly duplicated loci may have some alleles that are still functional and others that are inactive. The fixation of a pseudogene takes a long time.
The third type of pseudogene is the "unitary" pseudogene. Unitary pseudogenes are genes that have no parent gene. There is no functional gene in the genome that's related to the pseudogene.
Unitary psedogenes arise when a normally functional gene becomes inactivated by mutation and the loss of function is not detrimental to the organism. Thus, the mutated, inactive, gene can become fixed in the population by random genetic drift.
The classic example is the gene for L-glucono-γ-lactone oxidase (GULO), a key enzyme in the synthesis of vitamin C (L-ascorbate, ascorbic acid). This gene is functional in most vertebrate species because vitamin C is required as a cofactor in several metabolic reactions; notably, the processing of collagen [Vitamin C]. This gene has become inactive in primates so primates cannot synthesize Vitamin C and must obtain it from the food they eat.
A pseudogene can be found at the locus for the L-glucono-γ-lactone oxidase gene[GULOP = GULO Pseudogene]. It is a highly degenerative pseudogene with multiple mutations and deletions [Human GULOP Pseudogene]
This is a unitary pseudogene. Unitary pseudogenes are rare compared to processed pseudogenes and duplicated pseudogenes but they are distinct because they are not derived from an existing, functional, parent gene.
Note: Intelligent design creationists will go to great lengths to discredit junk DNA. They will even attempt to prove that the GULO pseudogene is actually functional. Jonathan Wells devoted an entire chapter in The Myth of Junk DNA to challenging the idea that the GULO pseudogene is actually a pseudogene. A few years ago, Jonathan McLatchie proposed a mechanism for creating a functional enzyme from the bits and pieces of the human GULOP pseudogene but that proved embarrasing and he retracted [How IDiots Would Activate the GULO Pseudogene] Although some scientists are skeptical about the functionality of some pseudogenes, they all accept the evidence showing that most psuedogenes are nonfunctional.
Of the three different kinds of pseudogenes, the easiest kind of pseudogene formation to understand is simple gene duplication followed by inactivation of one copy. [see: Processed pseudogenes for another type]
I've assumed, in the example shown below, that the gene duplication event happens by recombination between sister chromosomes when they are aligned during meiosis. That's not the only possibility but it's easy to understand.
These sorts of gene duplication events appear to be quite common judging from the frequency of copy number variations in complex genomes (Redon et al., 2006; MacDonald et al., 2013).
Let's look at the formation of a "processed" pseudogene. They are called "processed" because they are derived from the mature RNA produced by the functional gene. These mature RNAs have been post-transcriptionally processed so the pseudogene resembles the RNA more closely than it resembles the parent gene.
This is most obvious in the case of processed pseudogenes derived from eukaryotic protein-coding genes so that's the example I'll describe first.
In the example below, I start with a simple, hypothetical, protein-coding gene consisting of two exons and a single intron. The gene is transcribed from a promoter (P) to produce the primary transcript containing the intron. This primary transcript is processed by splicing to remove the intron sequence and join up the exons into a single contiguous open reading frame that can be translated by the protein synthesis machinery (ribosomes plus factors etc.).1 [See RNA Splicing: Introns and Exons.]
I define a gene as "DNA sequence that is transcribed to produce a functional product" [What Is a Gene? ]. Genes can encode proteins or the final product can be a functional RNA other than mRNA.
A pseudogene is a broken gene that cannot produce a functional RNA. They are called "pseudogenes" because they resemble active genes but carry mutations that have rendered them nonfunctional. The human genome contains about 14,000 pseudogenes related to protein-coding genes according to the latest Ensembl Genome Reference Consortium Human Genome build [GRCh38.p3]. There's some controversy over the exact number but it's certainly in that ballpark.1
The GENCODE Pseudogene Resource is the annotated database used by Ensembl and ENCODE (Pei et al. 2012).
There are an unknown number of pseudogenes derived from genes for noncoding functional RNAs. These pseudogenes are more difficult to recognize but some of them are present in huge numbers of copies. The Alu elements in the human genome are derived from 7SL RNA and there are similar elements in the mouse genome that are derived from tRNA genes.
There are three main classes of pseudogenes and one important subclass. The categories apply to pseudogenes derived from protein-coding genes and to those derived from genes that specify functional noncoding RNAs. I'm going to describe each of the categories in separate posts. I'll mostly describe them using a protein-coding gene as the parent.
The answers are the platypus and the opossum. The overall impression she conveys to the general public is that these species have not evolved for millions and millions of years.
I don't agree. I think it's important to teach the general public that such statements flatly contradict modern evolutionary theory. If, in fact, we discovered modern species that showed no signs of having evolved for millions of years, this would refute modern evolutionary theory.
The accepted minimal definition of evolution is ... [What Is Evolution?]
Evolution is a process that results in heritable changes in a population spread over many generations.
... or something similar like "change in the frequency of alleles in a population."
The main accepted mechanisms of evolution are natural selection and random genetic drift.
The only way positive natural selection1 can stop is if an organism is so perfectly adapted to its current environment (external and internal) that every possible mutation is either deleterious or neutral. That includes all metabolic processes and every structure in the cell.
Nobody could rationally advocate such a claim.
The only way to stop random genetic drift is if there's no such thing as a new neutral or nearly neutral mutation and all such variation in the population has been eliminated.
No evolutionary biologist could possibly make such a claim with a straight face.
It's easy to test such ridiculous claims by looking at the genomes of the opossum and the platypus. The evidence shows that they have evolved at the same rate as all other species.
The article actually mentions this problem ...
“'Unchanged' is a tricky word,” Nizar Ibrahim, a paleontologist at the University of Chicago and 2014 National Geographic Explorer, says via email.
With only fossils to go by, scientists can examine an ancient animal's skeletal structure, but it's not the whole story. Physiology and DNA change somewhat over time, he says, both through the basic process of evolution as well as random genetic changes.
That said, two mammals that have undergone the fewest evolutionary shifts are the platypus and the opossum, says Samantha Hopkins, associate professor of geology at the University of Oregon.
Liz Langley did not pick up on this comment so she missed a wonderful teaching moment.
It's possible that Liz Langley isn't aware of modern evolutionary theory and that she actually believes that evolution comes to a halt as long as species live in a relatively constant environment. It's possible that she disagrees with the minimal definition of evolution and prefers a definition that only counts significant changes in external phenotype. Or, it's possible that she thinks that National Geographic readers can't handle modern evolutionary theory. If it's the latter, I disagree.
1. You can't stop negative natural selection unless there are no new deleterious mutations. That's also impossible.
Casey Luskin: ... and, as we all know, or many ID the Future listeners probably know, for years Darwinian theorists and evolutionary scientists have said that our genomes ought to be full of junk if evolution is true
.....
Casey Luskin: So, Dr. Hunter, you think, just for the record, that in the long term there is going to be function found for probably the vast majority of the genome and so, maybe, you might call it a prediction you would make coming out of an intelligent design paradigm. Is that correct?
Cornelius Hunter: Yes, that's correct Casey, I'll definitely go on the record on that. Not to say I have a hundred percent confidence and also I wanna be clear that from a metaphysical perspective, from my personal belief, I don't have a problem wherever it lands. It doesn't matter to me whether it's 10% or 90% or any where in between or 100% ... just from the scientific perspective and just from the history of science and the history of what we've found in biology, it really does look like it's gonna be closer to 100 than zero.
Casey Luskin: Okay, great, I always like it when people put clear and concrete predictions out there and and I think that's very helpful.
I predict that about 90% of our genome will turn out to be junk DNA—DNA with no function. I base my prediction on the scientific perspective and the history of what we've found in biology. That's interesting because Cornelius Hunter and I are apparently reaching opposite conclusions based on the same data.
I also love it when people make predictions. Will the intelligent design paradigm be falsified if I turn out to be right?
Does it sound to you that Cornelius Hunter personally doesn't care if the prediction coming out of the intelligent design paradigm is correct or not?
1. How come in the podcast they never refer to Dan Graur as Dr. Graur? Isn't that strange?
... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.
Stephen Jay Gould Ontogeny and Phylogeny (1977)Back when the Nobel Prize in Chemistry was announced I was surprised to learn that it was for DNA repair but Phil Hanawalt wasn't a winner. I blogged about it on the first day [Nobel Prize for DNA repair ].
I understand how difficult it is to choose Nobel Laureates in a big field where a great many people make a contribution. That doesn't mean that the others should be ignored but that's exactly what happened with the Nobel Prize announcement [The Nobel Prize in Chemsitry for 2015].
In the early 1970s, scientists believed that DNA was an extremely stable molecule, but Tomas Lindahl demonstrated that DNA decays at a rate that ought to have made the development of life on Earth impossible. This insight led him to discover a molecular machinery, base excision repair, which constantly counteracts the collapse of our DNA.
Maybe it's okay to ignore people like Phil Hanawalt and others who worked out mechanisms of DNA repair in the early 1960s but this description pretends that DNA repair wasn't even discovered until ten years later.
By that time I was in touch with David Kroll who was working on an article about the slight to early researchers. He had already spoken to Phil Hanawalt and discovered that he (Hanawalt) wasn't too upset. Phil is a really, really nice guy. It would be shocking if he expressed disappointment or bitterness about being ignored. I'll do that for him!
OK, Larry. I assume you mean to say that I do not understand the basics of Darwinism. I challenge you, therefore, to demonstrate your claim.
This was the kind of challenge that's like shooting fish in a barrel but I thought I'd do it anyway in case it could serve as a teaching moment. Boy, was I wrong! Turns out that ID proponents are unteachable.
I decided to concentrate on Arrington's published statements about junk DNA where he said ...
I was alerted to this video by a post on Facebook. I had never seen it before. The occasion is the celebration of the 20th anniversary of McLean v. Arkansas— one of the legal victories of Americans who are fighting to keep creationism out of the classroom.
It's a 30 minute presentation by Stephen J. Gould on the fossil record. The event took place in February 2001, just a year before he died. You should watch it for many reasons—too many to mention them all here but here are some of the most important ones.
There are several different kinds of genes. Some of them encode proteins, some of them specify abundant RNAs like tRNAs and ribosomal RNAs, some of them are responsible for making a variety of small catalytic RNAs, and some unknown fraction may specify regulatory RNAs (e.g. lncRNAs).
This jumble of different kinds of genes makes it difficult to estimate the total number of genes in the human genome. The current estimates are about 20,000 protein-coding genes and about 5,000 genes for functional RNAs.
Aside from the obvious highly conserved genes for ubiquitous RNAs (rRNA, tRNAs etc.), protein-coding genes are the easiest to recognize from looking at a genome sequence. If the protein is expressed in many different species then the exon sequences will be conserved and it's easy for a computer program to identify the gene. The tough part comes when the algorithm predicts a new protein-coding gene based on an open reading frame spanning several presumed exons. Is it a real gene?
In my first post [Answering Barry Arrington's challenge: Darwinism] I established that Barry Arrington's version of "Darwinism" is actually "Neo-Darwinism" or the "Modern Synthesis." We all know why Intelligent Design Creationists would rather use "Darwinism"—this explains why they deliberately change the meaning to make it look like they understand evolution
Arrington's version of "Darwinism can be seen in the Uncommon Descentglossary. It focuses on natural selection as the mechanism of evolution and doesn't mention Neutral Theory of random genetic drift.
OK, Larry. I assume you mean to say that I do not understand the basics of Darwinism. I challenge you, therefore, to demonstrate your claim.
Today I'm feeling optimistic—life is good and this evening we're going to a nice restaurant for dinner with our favorite nephew.1 Let's try, once again, to convert this into a teaching moment. Hopefully, at least one or two ID proponents will learn something.2
Turn off your irony meters. Really ... I'm not kidding. They will never survive if you leave them on and follow the link to this post by Barry Arrington on Uncommon Descent.
The answer, of course, is “nothing.” Having studied Darwinism for over 20 years, I can tell you what it posits. Therefore, when I attack it, I am attacking the actual thing, not some distortion of the thing that exists nowhere but my own mind.
One of the most frustrating things about the current crop of Intelligent Design Creationists is that it's impossible to pin them down on what they really think happened in the history of life. We know that some of them are closet Young Earth Creationists so we can guess what they think. They may be arguing that bacterial flagella reveal the actions of a designer but they actually don't believe any of the data used to make that argument. They think that all species (or kinds) were created at once just a few thousand years ago.
Other Intelligent Design Creationists seem to believe in a different form of creation but who knows what it is? Take Stephen Mayer, for example, you can read his books from cover to cover and still not know what he thinks about the history of life. It's clear that the Cambrian Explosion is a big deal for him and it's clear that he thinks god is behind it all but he's remarkably noncommittal about what actually happened according to his interpretation of the evidence.
Let's think about the biochemical cost associated with adding some new piece of DNA to an existing genome. Michael Lynch has been thinking about this for a long time. He notes that there certainly IS a cost (burden) because the new bit of DNA has to be replicated. That means extra nucleotides have to be synthesized and polymerized every time a cell replicates.
This burden might seem prohibitive for strict adaptationists1 since everything that's detrimental should be lost by negative selection. Lynch, and others, ague that the cost is usually quite small and if it's small enough the detrimental effect might be below the threshold that selection can detect. When this happens, new stretches of DNA become effectively neutral (nearly neutral) and they can be fixed in the genome by random genetic drift.
The key parameter is the size of the population since the power of selection increases as the population size increases. Populations with large numbers of individuals (e.g. more than one million) can respond to the small costs/burdens and eliminate excess DNA whereas populations with smaller numbers of individuals cannot.
Canada has a new government under the Liberal Party and a new Prime Minister, Justin Trudeau. I'm very excited about this change. I'm a member of the Liberal Party of Canada and I voted for the Liberal Candidate in my riding.
One of the big changes is supposed to be increased transparency of government, more openness with the press, and a promise to base decisions on evidence and science. In other words, truth is supposed to be the new buzzword on Parliament Hill. Trudeau's new cabinet even has a Minister of Science, unlike previous cabinets.
This is our new Canadian Prime Minister walking to Rideau Hall with his new cabinet ministers for the swearing in ceremony where he officially takes over the government. It's very exciting. No Prime Minister has ever done this before today.
Now I may be wrong, but the more I read this, the more I think that reader Ant was right in his interpretation. What’s more galling is that the BBC is taking what “many scholars believe” as the gospel truth—pardon the pun—despite the fact that close scrutiny gives virtually no extra-Biblical evidence for a historical Jesus. I’m still convinced that the judgement of scholars that “Jesus was a real man” comes not from evidence, but from their conviction that the Bible simply couldn’t be untruthful about that issue. But of course we know of cases where myths grew up that weren’t at bottom derived from a historical individual.
There's nothing particularly wrong with what Jerry says. As far as I know the evidence that Jesus actually existed is not strong and, even more importantly, there's no independent evidence that he rose from the dead or performed miracles.
One of my wife's relatives just had her DNA tested by Ancestry.com and the results show that she is 61% Irish.1 She was (pleasantly) surprised so she shared the information with her relatives, including Ms. Sandwalk.
I was also surprised because I have a pretty extensive genealogy of my wife's side of the family and there's no ancestor from Ireland. Her grandparents—the aunt's parents—have typically Scottish surnames and they are the product of several generations of Scottish ancestors from a small community in Eastern Ontario.
I know of all the ancestors of the aunt (and my wife's mother) for five generations. That's 32 ancestors—their great-great-great-grandparents (Ms. Sandwalk's great4-grandparents). There were four ancestors born in England and 28 born in Scotland, mostly around Glasgow. The original settlers of this district all came from Scotland. That means that to a first approximation about 87% of the aunt's DNA comes from Scotland.
I'm one of those scientists who don't think that science as a way of knowing is restricted to investigating natural causes [John Wilkins Revisits Methodological Naturalism ]. I think that science can easily investigate supernatural claims and show that they are wrong. In theory, science might even show that the supernatural exists. Some (most?) philosophers agree. Maarten Boudry is the best known [Is Science Restricted to Methodologial Naturalism?].
This year is the tenth anniversary of Kitzmiller v. Dover Area School District. At that trial, the plaintiffs successfully convinced Judge Jones that intelligent design isn't a science because it invokes supernatural causes. The expert witnesses testified that, by definition, science is limited by methodological naturalism. I disagree with the expert witnesses at the trial and I agree with many leading philosophers that science is not restricted to methodological naturalism [Can Science Test Supernatural Worldviews? ].
For those of you who are interested in the evolution of the major animal phyla, let me introduce you to the topic.
See the little red circle on the phylogenetic tree on the right? That's what we're talking about.
Most of the major animal phyla are first observed as primitive fossils in the Cambrian about 540 million years ago. The fossils cluster around dates that only span a few million years (about 10 million years). This is the Cambrian Explosion (see little red circle).
There's considerable debate among evolutionary biologists about what caused this relatively rapid appearance of diverse and disparate large fossils. Intelligent Design Creationist, Stephen Meyer decided that such a debate casts serious doubt on evolution as an explanation for the history of life so he wrote a book called Darwin's Doubt.
