Monday, January 29, 2007
John Kasich Interviews Atheist Brian Flemming about the Blasphemy Challenge
We don't get FOX News up here so I've never seen this John Kasich dude in action. Watch him interview Brian Flemming, the originator of the Blasphemy Challenge, at [onegood move]. With people like John Kasich around we have a long way to go before the majority gives up their supersitutions and becomes rational.
Kasich just doesn't get it. One is left with the distinct impression that Kasich has never, ever, questioned his religious beliefs. In other words, he has been so thoroughly brainwashed that alternative viewpoints just don't exist for him. Disgusting.
[Hat Tip: RichardDawkins.NET]
Monday's Molecular #11
Name this molecule. You must be specific. We need the correct common name.
This is another easy one for everyone who has ever taken biochemistry. This compound is one of the most important energy molecules in living cells. We will discuss the very important reactions that result in synthesis of this molecule after you've been given a chance to identify it.
Sunday, January 28, 2007
What Is a Gene?
(Other definitions are at Discovering Biology in a Digital World, Pharyngula, and Greg Laden.)
The concept of a gene is a fundamental part of the fields of genetics, molecular biology, evolution and all the rest of biology. Gene concepts can be divided into two main categories: abstract and physical. Abstract genes are the kind we refer to when we talk about genes “for” a certain trait, including many genetic diseases. Most geneticists and many evolutionary biologists use an abstract gene concept.
Philosophers have coined the term “Gene-P” for the abstract gene concept. The “P” stands for “phenotype” indicating that this gene concept defines a gene by it’s phenotypic effects and not its physical structure.
Physical genes consist of stretches of DNA with a beginning and an end. These are molecular genes that can be cloned and sequenced. Philosophers call them “Gene-D” where “D” stands for “development”—a very unfortunate choice.
This essay describes various modern definitions of physical genes (Gene-D). I like to define a gene as “a DNA sequence that’s transcribed” but that’s a bit too brief for a formal definition. We need to include something that restricts the definition of gene to those entities that are biologically significant. Hence,
We could refine the definition by including RNA genes but that’s such a insignificant percentage of all genes that the refinement is hardly worth it. As we shall see, there are more significant limitations to the definition.
This "DNA sequence that's transcribed" definition describes a physical entity. Let’s examine a simple molecular gene to see how the definition applies.
This is a simple bacterial protein-encoding gene. The horizontal line represents a stretch of double-stranded DNA with the rectangular part being the gene. The gene is copied into RNA as shown by the arrow below the gene. This process is called transcription. Transcription begins when the transcription enzyme (RNA polymerase) binds to a promoter region (P) and starts copying the DNA beginning at the initiation site (i). The DNA is copied until a termination site (t) is reached at the end of the gene. According to my preferred definition of a gene, it starts at “i” and ends at “t.”
The part of the gene that’s transcribed includes the coding region, shown in black. This is the part of the gene that contains sequential codons specifying the amino acid sequence of the protein. At the beginning of the gene, called the 5ʹ (5-prime) end, there’s a short stretch of sequence that will be transcribed but not translated into protein. This 5ʹ untranslated region (5ʹ UTR) will contain various signals for starting protein synthesis.
The other end of the gene is called the 3ʹ (3-prime) end and there’s almost always a stretch that’s transcribed but not translated (3ʹ UTR). The 3ʹ UTR contains signals that cause transcription termination and also signals that regulate translation.
There are regions upstream of the promoter that control whether or not the gene is transcribed. These regions are called regulatory regions. They may contain binding sites for various proteins that will attach there in order to enhance the binding of RNA polymerase to the promoter. One of the differences between my preferred definition of a gene and others is that some other definitions include the promoter and the regulatory region.
There are two problems with such definitions. First, they’re not consistent with standard usage when we talk about the regulation of gene expression. We don’t say that only “part” of a gene is transcribed, which would be correct if we included the regulatory region in our definition of a gene. How often have we heard anyone say that regulatory sequences control the expression of part of the gene? That doesn’t make sense.
Second, by including regulatory sequences in the definition of a gene the actual extent of the gene becomes ill-defined. For most genes, we don’t know where all the regulatory sequences are located so we don’t know for sure where the gene begins or ends. Furthermore, there are some regulatory sequences, especially in eukaryotes, that are not contiguous with the gene and this leads to “genes” that are split into various pieces. It’s much easier to use a definition like “a DNA sequence that’s transcribed” because it defines a start and an end.
The organization of a typical eukaryote gene is shown below.
The main difference between this type of gene and a typical bacterial gene is the presence of introns and exons. These genes are transcribed from an initiation site to a termination site just like bacterial genes. When the RNA transcript is finished it undergoes an additional step called RNA processing. In that step, parts of the original transcript are spliced out and discarded. These parts correspond to the introns in the gene—shown as thinner rectangular region within the genes.
Note that the coding region (black) can be interrupted by these introns so the final messenger RNA (mRNA) cannot be translated until RNA processing is completed. The important point for our purposes is that the introns are part of the gene since they are transcribed.
My preferred definition has been used by molecular biologists for many decades but there are several other definitions that have been popular over the years. All of them have good points and bad points. I’ve already dealt with the definition that includes regulatory regions.
Some people still prefer a gene definition that corresponds to one used over half a century ago; namely, a gene is a sequence that encodes a polypeptide. This is the so-called one gene:one protein definition. It’s very old-fashioned. We’ve known for years that there are genes that do not encode proteins in spite of the fact that we commonly show protein-encoding genes whenever we describe typical genes. (As I did above.) There are genes for transfer RNA (tRNA), genes for ribosomal RNA, and genes for a large heterogeneous class of small RNAs. None of them have coding regions. The transcript is the functional product, often after RNA processing.
Because this old-fashioned definition is rarely used, the examples of alternative splicing producing different proteins pose no problem for modern definitions. These modern definitions refer to the transcript as the important product and not a protein.
There are exceptions to every generality in biology. Here’s a short list of gene examples that do not conform to my preferred definition.
Operons: In some cases adjacent “genes” are transcribed together to produce a large initial transcript containing several coding regions. In other cases the primary transcript is subsequently cleaved to produce multiple functional RNAs. In these cases it doesn’t make sense to refer to the co-transcribed genes as a single “gene.” Instead, we identify the stretches of DNA that correspond to a single functional unit as the “gene.” Thus, the lac operon contains three “genes” and the ribosomal RNA operons contain two, three, or four genes.
Trans-splicing: There are examples of “genes” that are split into pieces. The transcript from one piece is joined to the transcript from another to produce a functional RNA.
Overlapping Genes: Some “genes” overlap. This means that a single stretch of DNA can be part of two, and in at least one case, three genes.
RNA Editing: In some cases the primary transcript is extensively edited before it becomes functional. In the most extreme cases nucleotides are inserted and deleted. What this means is that the information content of the “gene” is insufficient to ensure a functional product and the assistance of other “genes” is required.
The concept of a gene is a fundamental part of the fields of genetics, molecular biology, evolution and all the rest of biology. Gene concepts can be divided into two main categories: abstract and physical. Abstract genes are the kind we refer to when we talk about genes “for” a certain trait, including many genetic diseases. Most geneticists and many evolutionary biologists use an abstract gene concept.
Philosophers have coined the term “Gene-P” for the abstract gene concept. The “P” stands for “phenotype” indicating that this gene concept defines a gene by it’s phenotypic effects and not its physical structure.
Physical genes consist of stretches of DNA with a beginning and an end. These are molecular genes that can be cloned and sequenced. Philosophers call them “Gene-D” where “D” stands for “development”—a very unfortunate choice.
This essay describes various modern definitions of physical genes (Gene-D). I like to define a gene as “a DNA sequence that’s transcribed” but that’s a bit too brief for a formal definition. We need to include something that restricts the definition of gene to those entities that are biologically significant. Hence,
A gene is a DNA sequence that is transcribed to produce a functional product.This eliminates those parts of the chromosome that are transcribed by accident or error. These regions are significant in large genomes; in fact, the confusion between accidental transcripts and real transcripts is responsible for the overestimates of gene number in many genome projects. (In technical parlance, most ESTs are artifacts and the sequences they come from are not genes.)
We could refine the definition by including RNA genes but that’s such a insignificant percentage of all genes that the refinement is hardly worth it. As we shall see, there are more significant limitations to the definition.
This "DNA sequence that's transcribed" definition describes a physical entity. Let’s examine a simple molecular gene to see how the definition applies.
This is a simple bacterial protein-encoding gene. The horizontal line represents a stretch of double-stranded DNA with the rectangular part being the gene. The gene is copied into RNA as shown by the arrow below the gene. This process is called transcription. Transcription begins when the transcription enzyme (RNA polymerase) binds to a promoter region (P) and starts copying the DNA beginning at the initiation site (i). The DNA is copied until a termination site (t) is reached at the end of the gene. According to my preferred definition of a gene, it starts at “i” and ends at “t.”The part of the gene that’s transcribed includes the coding region, shown in black. This is the part of the gene that contains sequential codons specifying the amino acid sequence of the protein. At the beginning of the gene, called the 5ʹ (5-prime) end, there’s a short stretch of sequence that will be transcribed but not translated into protein. This 5ʹ untranslated region (5ʹ UTR) will contain various signals for starting protein synthesis.
The other end of the gene is called the 3ʹ (3-prime) end and there’s almost always a stretch that’s transcribed but not translated (3ʹ UTR). The 3ʹ UTR contains signals that cause transcription termination and also signals that regulate translation.
There are regions upstream of the promoter that control whether or not the gene is transcribed. These regions are called regulatory regions. They may contain binding sites for various proteins that will attach there in order to enhance the binding of RNA polymerase to the promoter. One of the differences between my preferred definition of a gene and others is that some other definitions include the promoter and the regulatory region.
There are two problems with such definitions. First, they’re not consistent with standard usage when we talk about the regulation of gene expression. We don’t say that only “part” of a gene is transcribed, which would be correct if we included the regulatory region in our definition of a gene. How often have we heard anyone say that regulatory sequences control the expression of part of the gene? That doesn’t make sense.
Second, by including regulatory sequences in the definition of a gene the actual extent of the gene becomes ill-defined. For most genes, we don’t know where all the regulatory sequences are located so we don’t know for sure where the gene begins or ends. Furthermore, there are some regulatory sequences, especially in eukaryotes, that are not contiguous with the gene and this leads to “genes” that are split into various pieces. It’s much easier to use a definition like “a DNA sequence that’s transcribed” because it defines a start and an end.
The organization of a typical eukaryote gene is shown below.
The main difference between this type of gene and a typical bacterial gene is the presence of introns and exons. These genes are transcribed from an initiation site to a termination site just like bacterial genes. When the RNA transcript is finished it undergoes an additional step called RNA processing. In that step, parts of the original transcript are spliced out and discarded. These parts correspond to the introns in the gene—shown as thinner rectangular region within the genes. Note that the coding region (black) can be interrupted by these introns so the final messenger RNA (mRNA) cannot be translated until RNA processing is completed. The important point for our purposes is that the introns are part of the gene since they are transcribed.
My preferred definition has been used by molecular biologists for many decades but there are several other definitions that have been popular over the years. All of them have good points and bad points. I’ve already dealt with the definition that includes regulatory regions.
Some people still prefer a gene definition that corresponds to one used over half a century ago; namely, a gene is a sequence that encodes a polypeptide. This is the so-called one gene:one protein definition. It’s very old-fashioned. We’ve known for years that there are genes that do not encode proteins in spite of the fact that we commonly show protein-encoding genes whenever we describe typical genes. (As I did above.) There are genes for transfer RNA (tRNA), genes for ribosomal RNA, and genes for a large heterogeneous class of small RNAs. None of them have coding regions. The transcript is the functional product, often after RNA processing.
Because this old-fashioned definition is rarely used, the examples of alternative splicing producing different proteins pose no problem for modern definitions. These modern definitions refer to the transcript as the important product and not a protein.
There are exceptions to every generality in biology. Here’s a short list of gene examples that do not conform to my preferred definition.
Operons: In some cases adjacent “genes” are transcribed together to produce a large initial transcript containing several coding regions. In other cases the primary transcript is subsequently cleaved to produce multiple functional RNAs. In these cases it doesn’t make sense to refer to the co-transcribed genes as a single “gene.” Instead, we identify the stretches of DNA that correspond to a single functional unit as the “gene.” Thus, the lac operon contains three “genes” and the ribosomal RNA operons contain two, three, or four genes.
Trans-splicing: There are examples of “genes” that are split into pieces. The transcript from one piece is joined to the transcript from another to produce a functional RNA.
Overlapping Genes: Some “genes” overlap. This means that a single stretch of DNA can be part of two, and in at least one case, three genes.
RNA Editing: In some cases the primary transcript is extensively edited before it becomes functional. In the most extreme cases nucleotides are inserted and deleted. What this means is that the information content of the “gene” is insufficient to ensure a functional product and the assistance of other “genes” is required.
The Richard Dawkins Definition of a Gene Is Seriously Flawed
(This is an updated version of an article that I originally posted to talk.origins on Sept. 6, 1999)
We are interested in the correct definition of a "gene" (see ...). Part of the confusion is due to popular science writers who don't get it right. For example, Richard Dawkins does some serious handwaving in The Selfish Gene and he compounds it in The Extended Phenotype.
Dawkins knows that his defintion of "gene" in the Selfish Gene is unusual so he returns to the subject in The Extended Phenotype in his discussion of the selfish replicator. Dawkins is forced to concede that his use of the word "gene" is incorrect. That's why he says,
More handwaving,
The most reasonable definition of gene is that it is a piece of DNA that is transcribed but there are exceptions to everything in biology. Some genes are made of RNA, for example, and sometimes it's better to define a gene in terms of the protein it encodes. In no case is it reasonable to define a gene in terms of its ability to be selected or whether recombination can occur within it.
We are interested in the correct definition of a "gene" (see ...). Part of the confusion is due to popular science writers who don't get it right. For example, Richard Dawkins does some serious handwaving in The Selfish Gene and he compounds it in The Extended Phenotype.
Dawkins knows that his defintion of "gene" in the Selfish Gene is unusual so he returns to the subject in The Extended Phenotype in his discussion of the selfish replicator. Dawkins is forced to concede that his use of the word "gene" is incorrect. That's why he says,
I am happy to replace 'gene' with 'genetic replicator where there is any doubt.Nevertheless, he tries very hard to defend his point of view by claiming that geneticists and molecular biologists can't come up with a good definition of gene either. This leads him to make some very silly statements about genes and cistrons. He defines his genetic replicators in terms of alleles which means that they don't exist unless there is variation in the genome. He then goes on to restrict his discussion of changes in frequency to the results of natural selection, which means that his "genes" are effectively defined by the mechanism he prefers. This is why he quotes George Williams,
This is the rationale behind Williams's definition: 'In evolutionary theory, a gene could be defined as any hereditary information for which there is a favorable or unfavorable selection bias equal to several or many times its rate of endogenous change.'The hand-waving in The Selfish Gene is even more obvious,
....The Extended Phenotype p.89
In the title of this book the word gene means not a single cistron but something more subtle. My definition will not be to everyone's taste, but there is no universally agreed definition of a gene. Even if there were, there is nothing sacred about definitions. We can define a word how we like for our own purposes, provided we do so clearly and unambiguously. The definition I want to use comes from G.C. Williams. A gene is defined as any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection.In the new version of The Selfish Gene (1989) Dawkins adds a footnote where he again addresses his critics, especially Sewall Wright. Dawkins defends his definition of a gene as a unit of selection.
....The Selfish Gene p.28
More handwaving,
I am using the word gene to mean a genetic unit that is small enough to last for a number of generations and to be distributed around in many copies. ... The more likely a length of chromosome is to be split by crossing-over, or altered by mutations of various kinds, the less it qualifies to be called a gene in the sense I am using the term.
....The Selfish Gene (1989) p.32
I said that I preferred to think of the gene as the fundamental unit of natural selection, and therefore the fundamental unit of self-interest. What I have now done is to *define* [Dawkins' emphasis] the gene in such a way that I cannot really help being right!The fact that Dawkins uses the word "gene" in such a non-standard way is not an issue as long as one recognizes that the Dawkins "gene" has nothing to do with the genes that molecular biologists and geneticists talk about. It's not an issue as long as one doesn't try and pretend that Dawkins has avoided handwaving and "clearly" refuted the problems raised by his critics.
....The Selfish Gene (1989) p.32
The most reasonable definition of gene is that it is a piece of DNA that is transcribed but there are exceptions to everything in biology. Some genes are made of RNA, for example, and sometimes it's better to define a gene in terms of the protein it encodes. In no case is it reasonable to define a gene in terms of its ability to be selected or whether recombination can occur within it.
Jane Fonda Is Back
It's about time. Jane Fonda spoke at the Washington rally for peace yesterday. She said "I haven't spoken at an anti-war rally for 34 years. But silence is no longer an option." Jane is right. Silence is no longer an option. We need to get out of Iraq and Afghanistan.Many of us will remember when "Hanoi Jane" visited North Vietnam in 1972. Is it time for her to visit Iraq?
[Photo Credit: According to Wikipedia "This photograph was shot by a public affairs officer of the Peoples Republic of Vietnam, and released worldwide for distribution."]
Psychic Sylvia Browne Is Nothing but a Con Artist and a Fake
Anderson Cooper on CNN does something right. He exposes Sylvia Browne as a con artist. She told the parents of a missing boy that their son was dead but he turned up alive after four years. James Randi takes part in the debunking.
Now, if only we could get Larry King to admit that psychics are frauds ....
Free Love, the '60's, and Protein Synthesis
Most of us have seen this video of protein synthesis. It was made in 1971 (close enough to the '60's) at Stanford University and narrated by Paul Berg. This is a classic. Every student has to see it. (Much of the science is outdated but you don't watch it for the science.)
You have to wait until 5 minutes into the video to start seeing the student participation section on the outdoor field. This sort of thing was easy to organize back in 1971 but I can't imagine my students doing it today. Perhaps I'm wrong. Would any of you be interested in making an updated version?
All mimsey was the mRNA, and protein chain outgrabe ....Thanks to Living the Scientific Life for finding it on YouTube.
Saturday, January 27, 2007
Should We Pity America, or Hate It?
The Maher Arar case came to a close yesterday when the Canadian government agreed to a $10.5 million dollar settlement. The Prime Minister apologized for Canada's role in the sorry saga [`I wish I could buy my life back'].
In case you don't know, Arar is a Canadian citizen. He was arrested by the FBI in New York in 2002 on suspicion of terrorism and send to Syria to be tortured. He was released after almost a year and returned to Canada. Since then he has been cleared of all charges by a judicial inquiry.
The American government refuses to admit they made a mistake (a lawsuit is pending). Even more extraordinary, they refuse to remove Arar from their "no-fly" list in spite of the fact that the Canadian system has found him innocent. The FBI file has been reviewed by the Canadian government and there's nothing in there to warrant further suspicion.
All this is well known in Canada and Canadians are angry. Here's an excerpt from an article by Thomas Walkom on the font page of today's Toronto Star [U.S. security trumps freedom].
Ottawa's decision to compensate Canadian Maher Arar for its role in his unlawful imprisonment and torture contains a warning and a lesson.Yes, it's heartbreaking and I feel sorry for my American friends who know what's going on (e.g., Ed Brayton). But enough is enough. The refusal to admit that they, like we, were wrong about Maher Arar does not deserve our pity. It's just plain stupid and wrong.
The warning is that Canada and the U.S. are on fundamentally different paths when it comes to matters of terrorism and human rights. The lesson is that until Ottawa gets more aggressive with our friends in the war on terror, a Canadian passport won't mean much.
First the warning. The U.S. has chosen to subordinate the principles of individual freedom to what it sees as its security needs. It jails people indefinitely without charge, utilizes interrogation methods that the United Nations describes as torture, wages illegal wars and commits the very crimes against humanity it once helped to prosecute.
For America's friends, this is heartbreaking to watch.
America seems to have lost its way after 9/11. Its leaders are willing to sacrifice basic human rights in order to imprison and torture people who they suspect of terrorist activities. Most of them are innocent but that doesn't seem to matter.
Furthermore, America has no respect for its friends. Canada's system of justice is just as good as America's—probably better. If we find Arar innocent then America should have the decency to respect our decision and remove him from their list of suspect terrorists.
Science blogger Bora Zivkovic
The Nature interview with Bora Zivkovic is out [here]. I want to take this opportunity to thank Bora and everyone else for organizing the 2007 North Carolina Science Blogging Conference. It was lots of fun, I'm looking forward to next year already.
Here's a photo that Bora took of me and my daughter Jane at dinner on Friday night (January 19th). That's Cathy Davies (The Lab Cat) on my right. Bora tells me [here] that we were right under the John Edwards campaign headquarters. I wish I known, I would have popped up to say "hello."
Praying before City Council Meetings
Following up on a previous posting [Reciting the Lord's Prayer at City Council] I note that the Durham city council (west of Toronto) voted on Wednesday to make prayers before the meeting "voluntary." There was an excellent news clip about this on CityTV and you can watch it here. I'm particularly impressed with Mayor Bob Shapherd of Uxbridge (a member of the council) who declared that he is a non-believer and doesn't want to be a hypocrite when he's forced to recite something he doesn't believe. I'm embarrassed that there are Canadian politicians who are stupid enough to think that public recital of a Christian prayer is a good thing. I'm proud of those who challenged them.
My own city council in Mississauga also prays before meetings. I've written to my councillor, Katie Mahoney, but she hasn't replied.
[Hat Tip: Richard Dawkins]
Let's Help America: Make Florida the 11th Province
America is in trouble. I urge all Canadians to sign the petiton at Florida11 to make Florida the 11th province of Canada. We need to do our bit to prevent a repeat of the 2000 election crisis that got America in such trouble in the first place.
Friday, January 26, 2007
Lead in Lipstick Will Cause Cancer
Friday's Urban Legend: FALSEThere's an email message circulating that warns women against the dangers of lead in lipstick.
It's currently #9 on the 25 Hottest Urban Legends. (Incidently, the Barack Obama myth has moved up to #1; see Baracl Obama Is a Closet Muslim).
The message claims that lead causes cancer. This is not true. The message claims that lipstick contains lead. This is correct but the levels are way below those allowed by health rules in civilized countries [Easily Lead].
[Photo credit: Wikipedia, Creative Commons]
IDiots and the War
Yesterday Ed Brayton posted on DaveScot's silly notions about the war in Iraq [DaveScot's Ridiculous Arguments]. Ed goes into much more detail than I did on Wednesday [The IDiots Understand the War in Iraq]. The most interesting thing about Ed's posting is his description of the censorship imposed on the thread over at Uncommon Descent. If you go there you'll notice that the comments are closed. But they weren't closed yesterday. Find out from Ed what Mike Dunford did to force DaveScot to delete all comments.And you wonder why we call them IDiots?
Toyota RAV4 Jousting
This is too cool. Anyone want to try it with me? I'll drive. We can challenge a team of IDiots.
Thursday, January 25, 2007
Teaching Ethics in Science: Science v Technology (Part 2)
[Larry Moran: Part 1] [Janet Stemwedel: Part 1, Part 2]
The issue is whether we should be teaching "ethics" in science classes. The particular examples that we've mentioned are debating whether GM food is good or bad and discussing the consequences of the human genome project.
My concern is not so much whether these issues are topical or fun—they certainly are. I'm worried about the fact that they detract from my main purpose, which is to get students to appreciate science for it's own sake and not just because of some application it might have.
The issue is whether we should be teaching "ethics" in science classes. The particular examples that we've mentioned are debating whether GM food is good or bad and discussing the consequences of the human genome project.
My concern is not so much whether these issues are topical or fun—they certainly are. I'm worried about the fact that they detract from my main purpose, which is to get students to appreciate science for it's own sake and not just because of some application it might have.
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