Last December David Dobbs wrote an article entitled "Die, selfish gene die!" in which he promoted some really stupid ideas about evolution. Jerry Coyne wasted little time in showing why Dobbs was way off the mark.
Unfortunately, Dobbs didn't make the best case against the concept of the selfish gene and Jerry Coyne didn't recognize that there was a real problem.
Now the issue has resurfaced because Aeon has announced another dead horse that needs beating [Dead or Alive? Is it time to kill off the idea of the ‘Selfish Gene’? We asked four experts to respond to our most controversial essay].
Once again Jerry Coyne is up to the challenge, taking on four "experts" without breaking a sweat [The “selfish gene” redux: Aeon magazine collects opinion on the metaphor].
And, once again, everyone misses the real point.
Here's what Jerry says in his latest post.
I won’t reprise my criticisms, except to say that the metaphor of genes acting as if they are "selfish" when subject to natural selection remains perfectly good, whether or not those genes (or any bit of DNA) are part of the genome that makes proteins, regulates other genes, or comprises any bit of DNA that has the ability to get itself replicated more often than its competitors.
This is correct as far as it goes. The "selfish gene" is a reasonable metaphor if you want to think about natural selection and adaptation. It's quite reasonable to metaphorically describe genes as "selfish" in such cases.
However, I think that "selfish gene" is often used as a metaphor for all of evolution and not just for natural selection. I think that most people who read Dawkins' book take it to be about EVOLUTION and not just natural selection. They understand that Dawkins is promoting a gene-centric view of evolution—and that's okay—but they come away from reading the book by thinking that all genes are selfish.
As most of you know, I prefer to emphasize Evolution by Accident. That's not to say that natural selection (selfish genes) isn't important, it is. What I believe is that there is a lot more to evolution than just selfish genes and we should not use the selfish genes metaphor as a stand-in for all of evolution.
Once you grasp that idea, it becomes much less useful to use the term "selfish gene" as a metaphor for anything, even natural selection and adaptation. That's why I think we should stop using the term "selfish gene."
Denyse O'Leary on Uncommon Descent wonders Is “macroevolution” even a meaningful term? It’s time to ask.
Here's the problem as creationists see it ...
The evolution that Darwin’s theory accounts for (natural selection acting on random mutation) is, in the real world, small changes that don’t add up to much over the long term.
That is why the term "macroevolution" had to be invented. It was a leap of faith to assume that Darwinian "microevolution" would become "macroevolution" instead of just being washed out by other types of change (what usually really happens).
But gradually scientists are becoming less afraid to talk about this: Macroevolution apparently happens, but not by Darwinian means.
G’bye, Darwin. We packed the crumpets for ya.
Will it soon be: So long, Darwin-in-the-schools pressure groups? Gee, how they’ll be missed in the legislatures and courts.
No, wait, we’ll all be too busy figuring out what really happens in the history of life. It’s a fascinating story and now – for once – we might get to read it without all the interruptions.
I can't tell you how frustrating it is to see this kind of crap over, and over, and over. We have been trying to teach evolutionary biology to the IDiots for decades but they seem to be totally incapable of listening.
True, there was a time when biologists thought that Darwinian natural selection was all there is in evolution. They even thought that all of evolution, from changes within populations to the evolution of new phyla, could be explained solely by natural selection acting on allele frequencies within populations (Darwinism).
Most evolutionary biologists have moved on in the past half century and they now realize that macroevolution is a separate field that combines genetics, population genetics, geology, ecology and a host of other fields in order to explain the history of life. So, Denyse, it's true that macroevolution happens by means other than Darwinism even though natural selection is an important component of macroevolutionary explanations.
The only news here is that it takes IDiots so long to catch up with evolutionary biologists.
Back in the days of talk.origins, this topic (macroevolution) came up so frequently that I wrote a little essay to explain it in a way that even the most profound IDiot could understand. The latest version is from 2006: Macroevolution.
Wouldn't it be nice if the creationists could make an attempt to understand modern evolutionary theory instead of just repeating the same old tired arguments that they used 50 years ago?
The suggestion that macroevolution should be divorced from microevolution provides Creationists only with a debating point. It allows Creationists to say that there are some evolutonary theorists who distinguish the mechanisms studied in classical population genetics from those they take to be involved in large-scale evolutionary change ... But this is not to suppose that the distinction drawn by heterodox evolutionists is that favored by the Creationists.
Philip Kitcher (1982) p.150
The evolution of sexual reproduction is one of the great mysteries of biology. I've been teaching this to undergraduates for several decades but it seems that most undergraduates don't get the message. Most of them think that sex has been explained and the answer is that sexual reproduction generates diversity.
I usually give them some reviews to read and, invariably, the experts who write the reviews will say that sex is a great unsolved mystery. If the experts think that this is a mystery then why do so many people think they have the answer?
Here's what Douglas Futuyma says in the 2nd edition of Evolution (p. 340).
I am reliably informed that meetings of the Mississauga City Council1 still begin with a prayer. I'm not sure why city councilors feel the need for extra divine guidance since Mayor Hazel McCallion2 is already present in the room.
Like most places in Canada, Mississauga is a diverse community with a substantial number of nonbelievers and a substantial number of non-Christians. Prayer has no place in a secular society and beginning a City Council meeting with prayer sends out all the wrong messages. Imagine that you are a nonbeliever waiting to petition City Council over some grievance and you have to watch your council member praying before you can speak.
The evolution of recombination is part of the discussion. It's not necessarily the same as the evolution of sex but many of the explanations for the evolutionary origin of sex invoke homologous recombination.
When I asked my students to explain the evolution of sex they mostly came up with arguments about why it is advantageous to generate genetic diversity in a population. Some of this diversity requires recombination to create new combinations of alleles on the same chromosome. The problem with this argument is that for every new combination produced, an old one will be restored. As John Maynard-Smith pointed out in 1968, when genes/alleles are in linkage equilibrium then recombination does not result in a change in allele frequencies (i.e. evolution).
This led Joe Felsenstein to write the following in 1988.
It is worth noting that Maynard Smith's argument invalidates the earliest genetic argument for the evolution of recombination, that advanced by East (1918). That argument is also the one commonly found in textbooks, which tend to be a bit out of date (in this case, by over 50 years). East argued that recombination creates new genotypes. So it does. An AB/ab parent will have among its gametes not only the two types that formed it, AB and ab, but also Ab and aB if there is recombination between the two loci. But if the population is in linkage equilibrium, then somewhere else an Ab/aB parent will be undergoing recombination, which will remove Ab and aB gametes and replace them by AB and ab. These two processes will exactly cancel each other if the two types of double heterozygote, coupling (AB/ab) and repulsion (Ab/aB) are equally frequent. This will happen precisely when the population is in linkage equilibrium. In that case no new genotypes arise by recombination.
...
We have that anomalous situation that a detailed population genetic analysis analysis reveals not only that the standard explanation for the evolution of recombination will not work, but also that there is a good evolutionary reason for believing that modifiers will be selected to eliminate recombination.
Is it true that what students are being taught is wrong? What did Joe Felsenstein really mean?
Felsenstein, J. (1988) "Sex and the evolution of recombination." in The Evolution of Sex: An Examination of Current Ideas. R.E. Michod and B.R. Levin eds. 74-86. [PDF]
Last night I was at a small gathering of Liberal supporters at the Paramount restaurant on Yonge Street in Toronto. The event was organized by Omar Alghbra my former MP in Mississauga. The guest of honour was Liberal MP Marc Garneau who was Canada's first astronaut. He represents the Montreal riding of Westmount—Ville-Marie.
Marc Garneau is one of a small handful of MPs in the Federal Parliament who has a Ph.D. (Electrical Engineering, Imperial College of Science and Technology, London, England) He has always been a strong supporter of science and technology and I know that he is involved in forming science policy for the Liberals under Justin Trudeau. This was my chance to put in a good word for funding basic science so I made my pitch. I described to him how the current funding situation is hurting basic science research in the universities [Canada is destroying a generation of scientists].
It wasn't really necessary. Garneau is a strong supporter of basic science and, if elected, the Liberal Party intends to reverse the policies of the current Conservative Party under Stephen Harper. They will change the distribution of funds at NSERC and CIHR to support more curiosity motivated research and to move away from the emphasis on using science funding to support business. According to Garneau, they will also reverse the Harper decision to force NRC into short-term goal oriented technology development and return it to a broad organization that also invests in basic research.
I was impressed by the fact that Marc Garneau was just as passionate about basic research as I am. I'm confident that the Liberal Party understands the problem and will, if elected, take steps to improve the current situation. The next step is to make sure that the Harper government is booted out of office before they can do even more damage.
I think it's time we started being serious about the limitations of the RNA world as a possible explanation for the origin of life. It's simply not possible to imagine a scenario where the first catalysts are RNA molecules because that requires a primordial soups full of nucleosides and sugar molecules. It requires the spontaneous synthesis of nucleotides and their polymerization.
That ain't happening.
You can salvage the RNA world by postulating that it arose AFTER primitive metabolic pathways were established using peptide catalysts but that's the best you can do. There's a nice article in The Scientist that describes the problem [RNA World 2.0].
Here's a teaser ....
The RNA world, first posited by Francis Crick1 and others in the late 1960s, remains an attractive hypothesis. Many of the chemical hurdles that once challenged the laboratory synthesis of the molecule under presumed primordial conditions are being overcome, and in vitro evolution experiments are yielding RNA molecules that perform numerous functions, including copying themselves or other RNAs. "I don’t think there can be much doubt that RNA was a major central player as both a catalyst and an early replicator," says Nick Lane, a biochemist at the University College London whose research falls under the “metabolism first” label. "So the RNA world is absolutely correct, as far as I’m concerned, in that."
But the notion that RNA, on its own, spontaneously assembled and evolved on early Earth has fallen out of favor. More likely, whatever conditions spawned compounds as complex as nucleotides also generated other organics, perhaps early forms of modern amino acids and fatty acids, the constituent parts of proteins and membranes. "I’m not sure how many people anymore believe in a pure RNA world. I certainly don’t," says Lane. "I think the field has drifted away from that, and there’s now an acknowledgment it had to be ‘dirty.’ "
Changing Ideas About The Origin Of Life
Was the Origin of Life a Lucky Accident?
Monday's Molecule #231 [Monday's Molecule #231] was the Shine-Delgarno sequence found a few nucleotides upstream of the initiation codon in many bacterial mRNAs. It interacts (base pairs) with a sequence on the 3′ end of 16S RNA to help form the translation initiation complex. This means that bacteria can have polycistronic mRNAs (from operons) and internal translation initiation. The winners were Keith Conover and Nevraj Kejiou. That's two weeks in a row that an undergraduate from the University of Toronto has won. I will be taking them to lunch. I encourage undergraduates from far, far away to hurry up and send in an answer to this week's molecule!
This week's molecule (left) is covalently bound to the lysine side chain of a protein. It exists in two distinct configurations that can be interconverted by a well-known chemical reaction. Name the two different configurations (common names only) and explain the significance of the reaction.
Email your answer to me at: Monday's Molecule #232. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
Saturday night was the night when most people in North American turned their clocks forward one hour for "Daylight Saving Time."1 TV, radios, and newspapers are whining about the fact that everyone was going to lose an hour's sleep. Some of the comments on my radio station advise people to avoid driving today (Monday) because you might be suffering from sleep deprivation.
This all seems very strange to me. Is it true that most people are so unfamiliar with traveling across time zones that turning your clock back one hour is a really big deal?
And what's this about losing one hour's sleep? When I got out of bed on Sunday morning it was about one hour later (on the clock) than the time I usually wake up on Sunday morning. I didn't lose an hour's sleep. The only people who lost an hour's sleep on Saturday night are those who wake up every Sunday morning to an alarm clock. Are you one of those people?
It's a little bit different on Monday morning when, I imagine, most people have to wake up to an alarm clock in order to get to work. I'm not one of those people. However, even on Sunday night the only way you lose an hour's sleep is if you went to bed an hour later than normal.
Somewhere along the way I have lost an hour of my day but it's not going to come out of sleep time. That would be silly. If I ever feel sleep deprived I'll just go to bed earlier.
How about the rest of you? Do you really give up an hour of sleep in the days following the shift to Daylight Savings Time?
More accurately known as "Daylight Shifting Time."
Later on today I'm giving a talk at Western University (London, Ontario, Canada)1 The subject is blogging.
I realized while preparing my talk that there were lots of things I didn't know for sure so here are some questions that you may be able to help with.
Most popular biology blogs
I don't know for sure which biology blogs are the most popular. I'm pretty sure that Pharyngula is still on top with respect to the number of views per day and I'm pretty sure that Why Evolution Is True is in the top ten but what about others? Do any of you know?
Best biology blogs
The best blogs aren't necessarily the most popular. I have my own opinion about the best blogs but my fear is that I've missed some blogs that I should be reading. What do you think? What are the best biology blogs?
Why do you read and comment?
I've talked to a lot of bloggers so I'm pretty sure I have a good idea about why we write blogs. But I realized that I was much less sure about why people read blogs and why people comment on blogs. What do you get out of reading blogs and why do you post comments? Do you think all scientists and science students should read the science blogs? (I don't.)
Have blogs changed anything?
Have blogs had much of an impact on science? I can think of a few examples such as the Arsenic Affair and the ENCODE Publicity Hype Fiasco where bloggers had an impact but I'm not sure these are significant in the log run. Is blogging just another kind of social interaction that really doesn't change the way science is done?
1. Formerly the University of Western Ontario. The talk is in the North Campus Building room 114 at 11:30 am.
THEME:
Transcription
The Journal of Biological Chemistry (JBC) publishes a little booklet of the "best of jbc." The latest copy arrived in the mail a few days ago and it alerted me to a paper published one year ago on the structure of Escherichia coli RNA polymerase σ70 holoenzyme (Murikami, 2013).1
The control of transcription initiation is a very important topic in biochemistry and molecular biology and the events in E. coli are the model for transcription initiation in all other species. We know more about RNA polymerase and promoter sites in E. coli than in any other species.
Monday's Molecule #230 (Jan. 27, 2014) [Monday's Molecule #230] was 2-carboxy-3-ketoarabinitol 1,5-bisphosphate. It's an intermediate in the reaction catalyzed by ribulose 1,5-bisphosphate carboxylase-osygenase (Rubisco), the key enzyme in the Carvin cycle. This is the molecule created by adding CO2 to the 2-carbon atom of ribulose 1,5-bisphosphate. The winners were Bill Gunn closely followed by the first correct answer from an undergraduate, Ariel Gershon. Ariel is a student at the University of Toronto so it looks like I'm going to have to buy a lunch.
This week's molecule (below) is a sequence. Name the sequence in red and briefly describe it's function.
Email your answer to me at: Monday's Molecule #231. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)
This month's Carnival of Evolution is hosted by a BIOCHEMIST (yeah!) named "Lab Rat" (S.E. Gould) at Lab Rat. Read it at 69th Carnival of Evolution: Darwin’s Day Edition.
Welcome to the 69th edition of the Carnival of Evolution! As February 12th was Darwin’s birthday, this is a Darwin’s Day carnival edition. To start with there’s a celebration of all things Darwinian at Synthetic Daisies, and a letter to the man himself for his 205th birthday.
The next Carnival of Evolution will be at ????
If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.
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I forgot to post a link to last month's Carnival of Evolution. It was hosted by a computational biologist who posts at Byte Size Biology. Read it at Carnival of Evolution, February 2014 Edition.
Wow, I haven’t posted anything in quite a while. Things are busy outside blogoland. But committing this blog to the February edition of the Carnival of Evolution just made me do it, so here goes. We’ll do this by scales, bottom up.
The next Carnival of Evolution (#70, April, 2014) will be at some unknown place.
If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.
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There was a time when sequencing a gene was just about all you needed to get a publication. Getting a high quality sequence of a typical protein-encoding gene (cDNA) took several years of work—almost sufficient for a Ph.D. thesis.
By the 1990's, that was routine and you needed much more to get a paper published. The genome era had begun and a good paper in a high impact journal required the complete sequence of an entire genome.
Today, you can't get a genome sequence published because it's so easy that undergraduates can do it.
David Smith of Western University (London, Ontario, Canada) laments the death of the genome paper while recognizing that sequencing has probably been abused (Smith, 2013). He makes some good points ...
One of the drawbacks of genome papers, however, is that they can create a mindset of sequence first, ask questions later. I once attended a Masters thesis defense where the external examiner asked the candidate why he sequenced the chloroplast genome of this particular species and what hypothesis was he trying to test. The student, looking startled, answered, "Because the genome hadn't been sequenced before and we didn't know what it looked like." After the defense, I overheard the examiner in the hallway venting to another professor. "We've created a culture of serial genomicists," she exclaimed. "Everyone's jumping from one genome sequence to the next, looking to score a major publication."
Regardless of this opinion, genome papers have provided much of the raw data that have shaped our view of genetics and evolution over the past 20 years. And they can also be a joy to read. Many of my favorite journal articles are genome papers. I remember, when I was a grad student in phycology, eagerly awaiting publication of the genome for Chlamydomonas—the superstar of green algae—and reading it incessantly once it was released, gleaning new insights each time through. There is something intimate and personal in learning about a species' genome. And similarly, if you are part of the team describing the genome, there is a feeling that you're giving the readers a first glimpse at an uncharted territory, with its unique landscape of genes, introns and intergenic regions.
But all of this may be coming to an end. Next generation DNA sequencing techniques have made it easy, fast and cheap to sequence genomes. Today, just about any scientist can walk out their laboratory doors, point to a living thing and say, “I will sequence you!” High-throughput technologies have flooded the academic market with genome papers. And the top journals have responded by only accepting papers describing the most novel, earth-shattering genomes. The less spectacular genomes, much like B-movies, go directly to video, or rather directly to GenBank. This sequencing-vs-publishing arms race has been going on for a long time.
...
Is it time to write the genome paper obituary? Maybe not quite yet. Every now and then they still claw their way into top journals. But the end is not far off, and when it does come, I'm sure that I speak for all of us genome geeks when I say, "Farewell, GP. It was fun while it lasted."
I still like to read genome papers but lately I've been put off by the lack of reliable information in most of those papers. One of things I'm interested in is the number genes, especially the number of unique genes. Unfortunately, the annotation usually relies on computer-generated gene predictions and those are notoriously unreliable.
Smith, D.R. (2013) Death of the genome paper. Frontiers in Genetics 4:1-2. [doi: 10.3389/fgene.2013.00072]
