James Tour is an organic chemist. He is a Professor of Chemistry and Professor, Professor of Mechanical Engineering & Materials Science, and Professor of Computer Science at Rice University (Houston, United States). James Tour is attracting a lot of attention on the Intelligent Design Creationist websites because he is sympathetic to their main claim; namely, that evolution is wrong [see A world-famous chemist tells the truth: there’s no scientist alive today who understands macroevolution].
Tour is one of the few genuine scientists who signed the Discovery Institute’s "A Scientific Dissent from Darwinism" (2001) that stated, "We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged." (There are very,very, few biologists who signed.)
What exactly, does Jame Tour mean? He wrote an article on his website that explains his position: Layman’s Reflections on Evolution and Creation. An Insider’s View of the Academy. I think it's interesting to discuss what he said.
He begins with ...
It's been almost a year since I commented on an Nature article by Philip Ball [see DNA: Nature Celebrates Ignorance]. Here's part of what I wrote back then ...
The main premise of the article is revealed in the short blurb under the title: "On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball."
What nonsense! We understand a great deal about how evolution works at the molecular level.
The worst thing about the Nature article was the misuse of the Central Dogma of Molecular Biology. The second worst thing was the "revelation" that genes are regulated by regulatory sequences as if that was a new discovery. (He mentions the ENCODE results.)
I think the hardened version of the Modern Synthesis is inadequate to describe 21st century evolutionary biology. I think that it didn't adequately recognize Neutral Theory and random genetic drift and it didn't place enough emphasis on macroevolution and the possibility of hierarchical modes of evolution.
There are a whole host of scientists who want to overthrow the Modern Synthesis for a variety of other (stupid) reasons. Most of them have no idea that the Modern Synthesis has (or should have) been replaced 40 years ago.
Here's another example from last week's issue Science (March 7, 2014). Susan M. Rosenberg and Christine Queitsch have an article entitled "Combating Evolution
to Fight Disease" (Rosenberg and Queitsch, 2014). They begin with ....
The war between science and religion is fought on many fronts. One of the most remarkable campaigns is the attempt by religious zealots to discredit evolution (and science). We see this played out on creationist websites ranging from the most absurd Young Earth Creationist sites to the somewhat more subtle websites of the Intelligent Design Creationists.1
I can understand why believers want to defend their beliefs—we all do that. The part I don't get is the incredible stupidity of the main defenders of Intelligent Design Creationism and Young Earth Creationism. Not all of them, of course, but enough to make me slap my head.
Let's take Michael Egnor as an example. He is perfectly entitled to defend his Roman Catholic beliefs and to try and poke holes in evolution. But why does he have to use such stupid arguments? Why is such a person promoted on the main Intelligent Design Creationist website, Evolution News & Views (sic). Is he really the best they've got?
Let's look at his latest post: Clueless in Toronto. He begins with ....
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.
