The second episode of the new Cosmos series is Some of the Things That Molecules Do.
It's about evolution and it's not bad. I have four comments.
A missed opportunity. Natural selection is important and Neil deGrasse Tyson did a pretty good job of explaining it. It wouldn't have taken a big effort to mention that there's more to evolution than natural selection. He could, for example, have pointed out that some breeds of dogs are prone to certain genetic diseases or health problems because some bad mutations were accidentally fixed alone with the good ones. He could have pointed out that our eyes have a blind spot.
The Theory of Evolution is not a fact. Neil deGrasse Tyson said that the theory of evolution is a fact. This is not correct. Evolution is a fact. Evolutionary theory attempts to explain how evolution occurs. Some of the explanations, like natural selection, are facts but many aspects of modern evolutionary theory are still hotly debated in the scientific community.
We don't understand the origin of life. The episode closed with deGrasse Tyson saying the we don't understand how life began and there's nothing wrong with admitting that we don't know something. Excellent!
There are better ways of drawing DNA. I don't like the way DNA is pictured in the first two episodes, especially in the opening sequence. It looks like the bases grow out of the backbone and fuse to form base pairs. They could have drawn a more accurate representation without losing any visual appeal.
I give the episode a B+.
The winner is Philip Johnson from Switzerland.
This week's molecule (left) is actually a collection of molecules. Name all five molecules and tell me what they have in common from a biochemical perspective. Common names will do.
Email your answer to me at: Monday's Molecule #233. 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.)
Yesterday we watched two episodes of House of Cards and two of our favorite TV shows; Amazing Race and The Good Wife. We also watched a show about working on a Tudor farm and I watched the second episode of Cosmos.
According to Veronica Abbas, I wasted valuable time when I could have been reading [Recommended Reading]. She links to an article by Erin Kelley who says, Reading Books Doesn't Just Make You Literate: It Reduces Stress, Promotes Good Health, and Makes You More Empathetic. I haven't read a book in over four months and I haven't read a novel in years.
I'm doomed to be illiterate, stressed, in poor health, and the opposite of empathetic.1 It also explains why I don't volunteer to work for a non-profit organization.
1. I'm pretty sure Veronica would agree with "illiterate."
I think that universities are places where diversity of opinion should be encouraged and where fringe ideas should be protected. I'm very much opposed to letting outside interests (i.e. politicians and lawyers) decide what should and should not be taught on a university campus.
Clearly there are limits but those should be decided by faculty who understand the concept of academic freedom. It's not a good idea to offer astronomy courses on an Earth-centered solar system or geology courses based on the idea that the Earth is only 6000 years old. Those ideas are just too far out on the fringe. You're unlikely to find any university professors who want to teach such courses.
However, there are lots of other controversies that aren't so easily dismissed. If some of the more enlightened Intelligent Design Creationists want to teach a science course at my university, I would not try to prevent them. Just as I didn't try to prevent Michael Behe and Bill Dembski from speaking on my campus.
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.
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]
David Klinghoffer isn't impressed by the fact that the DNA of humans and bonobos is 98.6% identical in the areas that can be aligned. Here's what he says at: This Might Be the World's Most Underwhelming Evidence for Darwinian Evolution ...
Oh please. If there are any "creationists" out there who are running scared, they need not do so. The new article [by Chris Mooney] is titled "You Share 98.7 Percent of Your DNA with This Sex-Obsessed Ape," referring, of course, to the precious bonobo, a chimp-like ape famous for its progressive sexual habits. Just by itself, the genetic similarity between us and apes such as the bonobo is supposed to be of knockdown importance.
But what else would anyone expect, whether on a model of Darwinism, intelligent design, or creationism? Apes and humans are similar in many ways, and you don't need Darwinian evolution to see this.
This is a common argument from the IDiots. They assume that the intelligent designer created a model primate and then tweaked it a little bit to give chimps, humans, orangutans, etc. That's why the genomes of these species are so similar.
Unfortunately for them, there's a bit more to it than that. Their model of intelligent design also has to account for the fact that humans are more similar to chimps/bonobos than to gorillas and all three are about the same genetic distance from orangutans. This sequence data correlates with the fossil record over a period of about 10-15 million years.
It gets even worse for the IDiots. Evolutionary theory predicts that the rate of change should correspond to the mutation rate since most of the differences are due to neutral substitutions in junk DNA. We know that the mutation rate is about 130 mutations per generation based on our knowledge of biochemistry. This rate has been confirmed by direct sequencing of parents and children [Estimating the Human Mutation Rate: Biochemical Method] [Estimating the Human Mutation Rate: Direct Method].
If evolutionary theory (population genetics) is correct, and if David Klinhoffer and chimps/bonobos actually evolved from a common ancestor, then we should observe a correspondence between the percent similarity of Klinghoffer and chimps and the predicted number of changes due to evolution.
Let's see if it works.
The human and chimp genomes are 98.6% identical or 1.4% different. That difference amounts to 44.8 million base pairs distributed throughout the entire genome. If this difference is due to evolution then it means that 22.4 million mutations have become fixed in each lineage (humans and chimp) since they diverged about five million years ago.
The average generation time of chimps and humans is 27.5 years. Thus, there have been 185,200 generations since they last shared a common ancestor if the time of divergence is accurate. (It's based on the fossil record.) This corresponds to a substitution rate (fixation) of 121 mutations per generation and that's very close to the mutation rate as predicted by evolutionary theory.
Now, I suppose that this could be just an amazing coincidence. Maybe it's a fluke that the intelligent designer introduced just the right number of changes to make it look like evolution was responsible. Or maybe the IDiots have a good explanation that they haven't revealed?
Or maybe they're just IDiots who don't know what they are talking about.
Creationists are fond of mentioning people who are committed to creationism but still function as successful scientists. We saw an example in the debate between Bill Nye and Ken Ham. These creationist "scientists" are often physicians or engineers.
It seems obvious to most of us that engineers and physicians are not scientists. PZ Myers mentions this on his blog when he discusses the debate as reviewed by William Saletan: Saletan is at it again. Here's what PZ says ...
Engineers can practice real science, but an engineer is not the same thing as a scientist. I agree that creationists can be perfectly good engineers, but how can you trust the scientific acumen of someone who insists that the earth is only 6,000 years old? That says right there that they have no respect for the evidence. How can Saletan ignore Ham’s bogus distinction between historical and observational science, in which he flatly rejects any possibility of inference about the past from the present? This creationism is utterly incompatible with biology, anthropology, geology, astronomy, climate science, geochemistry, cosmology, and any other science that deals with cause and effect and history. These sciences apparently do not matter to Saletan, as long as engineers make satellites and doctors do surgery.
Saletan cites Ham’s videos as falsifying the claim that creationism is incompatible with science. Ken Ham makes a big deal of this, too.
This would be unremarkable except that Jason Rosenhouse disagrees [Saletan vs. Myers on Nye vs. Ham]. Here's what Jason says ...
Oh for heaven’s sake! Engineers are scientists. Full stop. Are you really that desperate to deny that a creationist could ever make a contribution to science that you will sink to this level of insult and idiocy? (Yes, it is insulting to suggest that engineers are not scientists.)
Engineers have a Bachelor's degree in engineering and they typically work for a construction company or in the IT department of a large corporation. They are not scientists. Full stop.
It's true that some engineers do science but usually they have a higher degree in engineering and usually they are academics. There's no possible way you could assume that all engineers are scientists just because they are licensed engineers and wear the ring. I'm sorry, Jason, but you are wrong.
Similarly, the typical physician has a private practice at a strip mall in the suburbs. They have an M.D. degree that can be earned right out of high school (in Europe). They are not scientists.
There are some physicians who are scientists and some of them have earned Nobel Prizes. They are the exceptions, not the rule. It's ridiculous to assume that everyone with an M.D. is a scientist.
Here's a five year old video where Richard Dawkins points to molecular phylogenies as powerful evidence of evolution. He wonders how any creationist could deny the evidence of evolution and suggest that "a mind like that is a disgrace to the human species."
He must have been thinking about Cornelius Hunter because Hunter has resurrected the video in order to show why Dawkins is wrong [Richard Dawkins: How Could Anyone "Possibly Doubt the Fact of Evolution"]. Watch the video and then read what Cornelius Hunter says. You'll recognize some elements of truth in his criticism but you'll also recognize a common creationist fallacy; namely, an inability to see the forest because you've been staring too long at the bark on trees.
What is amazing is the evolutionist’s high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”
An even more severe problem is that in many cases no comparison is even possible. The molecular sequence is found in one species but not its neighbors. When this problem first became apparent evolutionists thought it would be resolved as the genomes of more species were decoded. No such luck—the problem just became worse. Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”
Short genes that produce what are known as microRNA also contradict Dawkins’ high claim. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”
Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”
And yet in public presentations of their theory, evolutionists present a very different story. As Dawkins explained, gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd. And then Dawkins chastises anyone who “could possibly doubt the fact of evolution.” Unfortunately this sentiment is typical. Evolutionists have no credibility.
Gary Gutting interviews atheist Louise Antony in the New York Times [Arguments Against God]. Here's part of the interview ...
L.A.: Knowledge in the real world does not entail either certainty or infallibility. When I claim to know that there is no God, I mean that the question is settled to my satisfaction. I don’t have any doubts. I don’t say that I’m agnostic, because I disagree with those who say it’s not possible to know whether or not God exists. I think it’s possible to know. And I think the balance of evidence and argument has a definite tilt.
G.G.: What sort of evidence do you have in mind?
L.A.: I find the "argument from evil" overwhelming — that is, I think the probability that the world we experience was designed by an omnipotent and benevolent being is a zillion times lower than that it is the product of mindless natural laws acting on mindless matter. (There are minds in the universe, but they’re all finite and material.)
The argument from evil goes like this ...
- Assume that supernatural, omnipotent beings exist.
- Assume that they are kind and benevolent and they have the power and desire to create human societies that will be kind and good.
- Therefore, because evil is commonplace, one of the assumptions must be wrong.
An atheist is concerned about whether supernatural beings exist so why in the world would they pay any attention to the premises of this argument? If I were to accept the premise that supernatural omnipotent beings exist then the argument from evil simply leads to the conclusion that the supernatural beings are evil (like Satan) or they don't much care about us, like the Greek gods.
The argument from evil says nothing about whether gods exist or not. It only refers to particular kinds of gods and the only way an atheist should pay any attention to it at all is if they are willing to concede that some sort of gods must exist. Then, and only then, can they enter into a discussion about what kinds of gods exist. In that sense, the argument from evil is about as useful as the Courtier's Reply.
I wish atheists would stop discussing the argument from evil because all it does is show that some gods are possible while others are unlikely. I do not see why Louise Anthony finds the argument convincing because it's perfectly consistent with the existence of Satan.
It's also perfectly consistent the god of the Old Testament (see above). That god is exactly the sort of god that that would create a human society full of evil. Humans are behaving just like the god they worship. What's the problem?
A meeting on macroevolution was held at the Field Museum of Natural History in Chicago in October 1980. Normally these meetings would not attract much attention from the press but in this case there was an article published in Discover a month before the meeting took place that suggested something revolutionary was in the wind. Stephen Jay Gould discusses the episode in The Structure of Evolutionary Theory (pp. 981-986).
The article in Discover referred to "growing dissent from the prevailing view of Darwinism" and mentioned that there would be a meeting in Chicago. As a result of this article, a bunch of journalists turned up at the Chicago Macroevolution meeting expecting fireworks.
There was a lot of talk about punctuated equilibria at the Chicago meeting and how the ideas of Eldredge and Gould conflicted with the gradualism that was part of traditional Darwinian evolution. This is complicated stuff so it's no wonder that many journalists misinterpreted the discussion as support for the idea that evolution was being challenged as the creationists claimed.
My students wrote the midterm test today. Here are the questions. They had to answer the first question and 4 other questions (out of 5). How would you do?
- What’s the most important new thing about molecular evolution that you have learned in this course so far? Explain your answer by describing your "important new thing."
- If mutation rates are relatively constant then why does the molecular clock tick at different rates in different proteins?
- Many evolutionary biologists think that population genetics is the key concept in understanding evolution but biology students often complete several years of courses without ever learning about effective population sizes, mutation rates and the importance of random genetic drift. Why? Is it because population genetics is not a necessary key concept in evolution?
- Grad students at this university publish a journal called Hypothesis. A few years ago (2005) there was a student who wrote ...
I am a grad student, and long hours at the bench have got me thinking of other things lately, including the idea of marriage. I came up with a few criteria to direct me on my quest for a wife, and near the top of the list was that she needs to know what a gene is. I thought that this would be a reasonable thing to ask for. I like learning about how we and the rest of life work, and knowing how, in a general sense, cells are programmed to do what they do is a pretty good indicator of similar interest. My friends, however, disagreed with me, and on several occasions, as I shared my list, I feared that things were going to get violent. They argued that I will never get married with such a short-sighted and elitist attitude.
Imagine that you would only seek partners who knew what a gene was. What definition would you require and why?
- What’s the best evidence that a substantial amount of our genome is junk?
- Imagine that you are teaching a class and you ask students to calculate a mutation rate in humans based on what they know about biochemistry. What mistakes are they most likely to make and why?
Last week I commented on whether bigots should be given permission to discriminate against gays just because the bigots belong to a religion that promotes bigotry [The Kansas anti-gay bill]. My opinion is that societies should not tolerate bigotry no matter what motivates people to discriminate. I said ...
I read some newspaper articles, and some blog posts, that stated the obvious. It is totally wrong, all the time, to discriminate against someone based on their sexual preferences. If they use religion as an excuse then they should re-evaluate their religion. There is NEVER a time when an enlightened society should tolerate, let alone legalize, bigotry. I guess it's almost impossible to come out and say this on television, or maybe I'm just watching the wrong channels (mostly FOX and CNN).
What I mean is that enlightened societies will almost always reach a consensus on discrimination against minorities. They will decide that society functions best when all types of discrimination are bad and should not be tolerated.
I'm currently in Los Angeles visiting the grandchildren so I'm a bit more exposed to American culture than normal. I watched several discussions on the Kansas anti-gay bill on television and one thing struck me as highly unusual.
For the sake of non-Americans, let's begin with a description of the bill passed by the Kansas House, which is dominated by Republicans. Here's what Bill 2453 says ...
Notwithstanding any other provision of law, no individual or religious entity shall be required by any governmental entity to do any of the following, if it would be contrary to the sincerely held religious beliefs of the individual or religious entity regarding sex or gender: (a) Provide any services, accommodations, advantages, facilities, goods, or privileges; provide counseling, adoption, foster care and other social services; or provide employment or employment benefits, related to, or related to the celebration of, any marriage, domestic partnership, civil union or similar arrangement; (b) solemnize any marriage, domestic partnership, civil union or similar arrangement; or (c) treat any marriage, domestic partnership, civil union or similar arrangement as valid.
In other words, if you are a bigot then the state will protect you from prosecution as long as you claim that your bigotry is based on religion.
The bill was expected to pass through the Kansas Senate and signed into law by a redneck governor. Fortunately for Kansas, the Republican-dominated senate decided that Kansas should drop out of the competition for most stupid state and they declined to pass the bill [Kansas Senate Comes To It’s Senses And Nixes Extreme Anti-Gay Legislation ].
That's not what I want to talk about. What I witnessed on the American TV channels was a debate over the legality of discrimination of gays. The discussion hinged on whether it was legal for an anti-gay bigot to refuse to serve a gay couple in a restaurant or whether an anti-gay bigot could refuse to bake a wedding cake for a gay couple. Almost everyone I saw on TV agreed that it was perfectly okay for Americans to be anti-gay bigots, especially if their bigotry was related to their belief in God. The only serious question seemed to be whether there were legitimate times when anti-gay bigots could express their bigotry in public.
I read some newspaper articles, and some blog posts, that stated the obvious. It is totally wrong, all the time, to discriminate against someone based on their sexual preferences. If they use religion as an excuse then they should re-evaluate their religion. There is NEVER a time when an enlightened society should tolerate, let alone legalize, bigotry. I guess it's almost impossible to come out and say this on television, or maybe I'm just watching the wrong channels (mostly FOX and CNN).
I'm reminded of a statement by Winston Churchill about Russia; "Russia is a riddle wrapped in a mystery inside an enigma." That's the way I feel about the United States. There's such a huge difference between Boston and Texas that I wonder how they can both continue to exist in the same country.
An old high school friend of Ms Sandwalk sent me the link to this video by Dirk Murray "Baba" Brinkman, Jr. He is the son of my friend's local MP, Joyce Murray (Liberal, British Columbia).
I hesitated to post in on Darwin Day but now that other blogs have linked to it, I want to use this opportunity to raise two important questions.
- The video promotes "Darwinism" as the only solution to evolution. This is wrong, but is there value in lying about this for a greater cause? Is it possible to make an effective video like this without distorting the science?
- I'm very uneasy about promoting Darwin worship, partly for the reason that there's more to evolution than what Darwin wrote in 1859 and partly for the reason that it smacks of religion. What do you think? Should we be pushing "Darwin Day"?
M=
PZ Myers posted an interesting article on The state of modern evolutionary theory may not be what you think it is. He makes the point that there's more to evolution than natural selection.
I think this is an important point but I would not explain it the same way as PZ. He focuses attention on Neutral Theory and the fact that neutral, or nearly neutral, mutations are fixed by random genetic drift. Here's how he describes it ...
First thing you have to know: the revolution is over. Neutral and nearly neutral theory won. The neutral theory states that most of the variation found in evolutionary lineages is a product of random genetic drift. Nearly neutral theory is an expansion of that idea that basically says that even slightly advantageous or deleterious mutations will escape selection — they’ll be overwhelmed by effects dependent on population size. This does not in any way imply that selection is unimportant, but only that most molecular differences will not be a product of adaptive, selective changes.
The debate over adaptationism is a debate over mechanisms of evolution. Random genetic drift is a mechanism of evolution that results in fixation or elimination of alleles independently of natural selection. If there was no such thing as neutral mutations then random genetic drift would still be an important mechanism.
Let's say you have a clearly beneficial mutation with a huge selection coefficient of 0.1 (s = 0.1). Population genetics tells us that the probability of fixation is 2s or, in this case, 20%. That means that the allele will be eliminated from the population 80% of the time. That's random genetic drift. Similarly, some fairly deleterious mutations can sometimes be fixed by random genetic drift.
Random genetic drift is a mechanism of evolution that was discovered and described over 30 years before Neutral Theory came on the scene.
What Neutral Theory tells us is that a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection. The conclusion is inescapable. Random genetic drift is, by far, the dominant mechanism of evolution.
Many people seem to equate Neutral Theory with random genetic drift. They think that random genetic drift is only important when the alleles are neutral (or nearly neutral). Then they use this false equivalency as a way of dismissing random genetic drift because it only deals with "background noise" while natural selection is the mechanism for all the interesting parts of evolution. I think we should work toward correcting this idea by separating the mechanisms of evolution (natural selection, random genetic drift, and others) from the quality of alleles being produced by mutation (beneficial, detrimental, neutral).
The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there's more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don't understand evolution.
I want to draw your attention to: Genomics researchers astonished to learn microarrays still exist. I especially like this comment from the author (jovialscientist) ...
In recent years, RNA sequencing (RNA-Seq) has been favoured over microarrays. This new technology, using next-generation sequencing, is slightly more accurate, and nations have recently declared war over which is the best aligner to use.
In a recent poll, 98% of researchers answered "next-generation sequencing" to every single question – even their name, age and job title. The new science of "sequence first, think later" has been coined "nextgenomics".
The atheists and skeptics had a wonderful time last Friday night. That's because the debate over "Is There a God?" was a tremendous defeat for Roman Catholics who turned out in droves to hear Philip Cleevely make the case for god.
Cleevely's only argument goes like this:
- The world began from nothing.
- That's very mysterious.
- Therefore, god(s) exist.
Justin Trottier did a very good job for the skeptic point of view. In particular, he made it very clear that he was NOT defending the proposition that gods do not exist. That's not what he means by atheism. He made it very clear that the burden of proof was on those making the extraordinary claim (god exists). He had to do this because rather than provide evidence for the existence of god(s), Cleevely kept trying to show that materialism.naturalism could not prove the nonexistence of gods.
I'm pretty sure that Cleevely didn't get it. I think he is committed to the idea that atheism means the denial of god(s) and he couldn't wrap his mind around the idea that he might be wrong.
The other point he (Cleevley) was trying to make was that science absolutely requires "something" in order to work. Since the universe began from "nothing" that means that it's beyond science. Again, this is an argument about the possible limitations of science but it says absolutely nothing at all about the case for the existence of god(s).
I think that most of the audience, even the Christians, realized that the priest was avoiding the question. As I said, Justin did an excellent job of steering the debate back to the main topic whenever possible. Near the end of the debate, Justin pointed out that Phillip Cleevely had not made much of a case and that the only evidence he had presented was not much more than philosophical babble. Justin didn't go on about this—just the right amount of harsh criticism—but it had to be said.
I'm pretty sure I wouldn't have been so kind.
Two other issues came up. Cleevely demanded that Justin explain where morality came from and where rational thought came from. Justin did a pretty good job but added that we don't have all the answers. He then assumed that Cleevely did have the answers but it turns out that Cleevely was not making the case for god based on the origin of morality or rationality. He said that those topics were too complicated—maybe they could be covered in another debate. The point of his questions was to show that science doesn't have all the answers. The implication is that because science doesn't have all the answers then god exists but Cleevely was clever enough (or stupid enough?) to avoid saying this.
Finally, Cleevely is an ordained priest and the moderator kept referring to him as "Father" whereas Justin was addressed as "Justin." There was a big difference between the respect that the moderator showed for Father Cleevely and for atheist Justin Trottier.
I imagine that it's impossible to avoid "Father" in a debate sponsored by Roman Catholics. His opponent should have been addressed as "Mr. Trottier."
There are still a few tickets available. Email me ASAP.
Michael Egnor is a brain surgeon who doesn't like evolution. Egnor isn't a scientist so why does it matter so much to him?
Listen to this podcast where Casey Luskin interviews Michael Egnor: Dr. Michael Egnor on Debating Intelligent Design. You may want to turn off your irony meter.
Egnor is afraid of evolution for exactly the right reasons. It's because evolution (and science) threaten his worldview. Science tells us that we don't have free will—at least not the kind of free will that Christians demand. Science tells us that there's no such thing as moral absolutes that are dictated by god(s). Science is materialistic and it may be the only valid way of knowing.
No wonder he's scared. Michael Egnor is a Roman Catholic and he knows that evolution threatens his religion.
You'll probably enjoy hearing Egnor and Luskin talk about atheist blogs and about the high quality of science writing on Evolution News & Views. Casey Luskin (lawyer) and Michael Engor (physician) are responsible for some of that high quality science writing.
David Klinghoffer really likes the podcasts. Here's his review at: Listening to Neurosurgeon Michael Egnor on the Brain and Intelligent Design, Rubik's Cube and Jerry Coyne's Blog.
I've exchanged many emails with brain surgeon and ENV contributor Dr. Michael Egnor, but I had never actually heard his voice till now. It's a good voice, which is vital for a physician, mellow yet authoritative, with the correct pitch and timbre. Egnor's stellar academic and medical background aside, I've often thought that, if you had no other information about a healthcare provider, what you don't want is a doctor with the wrong kind of voice.
Now you can hear Egnor as I just did in this fascinating new series of podcasts in which he is interviewed by Casey Luskin. Their themes include evidence of intelligent design in the complexity of the brain, but no less so in the simplest creature, a bacterium. Dr. Egnor compares that design to the solution of a Rubik's Cube. It doesn't happen by chance.
Egnor also talks about the unusual window that Jerry Coyne provides into the mind of a materialist, which is why his name comes up here often. Coyne, unlike many Darwin apologists, doesn't self-censor. You don't have to wonder: What does he really think about, for example, personal responsibility. Because he tells you! Whatever else Coyne may be, he's no weasel. For that, Egnor expresses his gratitude and -- yes, appropriately.
I'm disappointed that Egnor said nothing about me even though he posts quite a few comments on Sandwalk. Guess I don't get much respect.
I wonder why David Klinghoffer didn't mention Casey Luskin's voice?
Jason Rosenhouse also read the accommodationist article by Phil Plait [The Creation of Debate] and he also sees the problem.
I argued that, contrary to what Phil Plait believes, evolution is a threat to all superstitious beliefs, including those of theistic evolution creatinists (see my post at: The real war is between rationalism and superstition).
Read Jason Rosenhouse's post at: It’s Not Just Fundamentalist Religion That Has A Problem With Evolution. Here's the important part ....
So, after all, that, let us return to Plait’s argument. He tells us that the problem is too many people perceiving evolution as a threat to their religious beliefs. Indeed, but why do they perceive it that way? Is it a failure of messaging on the part of scientists? Is it because Richard Dawkins or P. Z. Myers make snide remarks about religion? No, those are not the reasons.
It is because these people have noticed all the same problems the scholars of Darwin’s time were writing about. It is because evolution really does conflict with their religious beliefs, but not because of an overly idiosyncratic interpretation of one part of the Bible. It is because the version of evolution that so worried the religious scholars of Darwin’s time, that of a savage, non-teleological process that produced humanity only as an afterthought, is precisely the version that has triumphed among modern scientists. And it is because the objections raised to that version of evolution in the nineteenth century have not lost any of their force today.
So I think the issue is just a tad more complex than Plait suggests. It manifestly is not the case that only the most narrow of fundamentalists has a problem with evolution. Evolution challenges the Bible, refutes the argument from design, exacerbates the problem of evil, and strongly challenges any notion that humanity plays a central role in creation. These are not small points, and Plait needs to acknowledge them.
I hope Phil Plait is listening.
I hope Ken Miller, Francis Collins, and Simon Conway-Morris are listening. They are not on my side in this war.
You're probably wondering why I would ask a question like, "Does an understanding of evolution help scientists understand the secrets of biology?" It's not my question. It's a paraphrase of a question asked by someone who goes by the pseudonym "PaV" on Uncommon Descent. Here's the full context from her post: Does Evolutionary Theory Really Help Scientists?
For a number of years, many of us at UD have made the argument that evolutionary theory, in practice, is of almost no help whatsoever in getting at the secrets of biology. I’ve taken the position personally that it actually hurts, and that it is not a matter of indifference to the study of biology whether evolution is employed or not. ID is the way to go.
Now, besides the fact that she is an IDiot, you may be asking why anyone would write such a thing.
Here's the scoop. Someone was looking at unknown RNAs in zebra fish and discovered that one of them encoded a protein that hadn't previously been characterized. This sort of thing happens all the time in various species so why is PaV so excited?
Here's the answer ...
They’ve studied this embryonic stage for 20 years, and couldn’t figure out the decisive signals for initiation of the gastrula. They had to look to “non-coding” RNA, i.e., “junk DNA,” in order to solve their new found secret.
And why didn’t they study “junk DNA” before? Well, evolutionary theory posits that it is “junk” (their word, not ours), so why investigate.
See? Evolutionary theory actually impedes scientific progress. And you wonder why we call them ....
