I love it when new things are discovered, especially if they concern biochemistry. I'm always on the lookout for exciting discoveries that are going to make it into the next edition of my textbook.
That's why my eyes lit up (not!) when I saw this headline in Biology New Net: New mechanism in gene regulation revealed. Here's the teaser ...
The information encoded in our genes is translated into proteins, which ultimately mediate biological functions in an organism. Messenger RNA (mRNA) plays an important role, as it is the molecular template used for translation. Scientists from the Helmholtz Zentrum Muenchen and the Technische Universität Muenchen, in collaboration with international colleagues, have now unraveled a molecular mechanism of mRNA recognition, which is essential for understanding differential gene regulation in male and female organisms. The results are published in the renowned scientific journal Nature.
It took me a few minutes to track down the article because there weren't many hints in the press release. Turns out it still hasn't appeared in the print copy but it's available online.
Hennig, J., Militti, C., Popowicz, G.M., Wang, I., Sonntag, M., Geerlof, A., Gabel, F., Gebauer, F., and Sattler, M. (2014) Structural basis for the assembly of the Sxl–Unr translation regulatory complex. Nature published online Sept. 7, 2014 [doi:10.1038/nature13693]
The "new mechanism" is the binding of a protein to mRNA to block translation.
I suppose it depends on your definition of "new." We've been teaching undergraduates about this for over thirty years.
There's nothing in the paper about a new mechanism of gene regulation and there's no evidence in the press release that any of the authors make such a claim.
Biology News Net has become a joke. It's rare to see a paper that it hasn't mangled or a press release that it hasn't fallen for, hook line and sinker. I read it for amusement.
A recent report began with ... [Parts of genome without a known function may play a key role in the birth of new proteins]
Researchers in Biomedical Informatics at IMIM (Hospital del Mar Medical Research Institute) and at the Universitat Politècnica de Catalunya (UPC) have recently published a study in eLife showing that RNA called non-coding (lncRNA) plays an important role in the evolution of new proteins, some of which could have important cell functions yet to be discovered.
That sounds intriguing. Maybe I should read the paper even though it's in eLife.
It took a little more work than I expected, but eventually I found the paper (Ruiz-Orera et al., 2014). Here's the abstract.
Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs are lineage-specific and do not yet have a known function. In this study, we test the hypothesis that they may act as a repository for the synthesis of new peptides. We find that a large fraction of the lncRNAs expressed in cells from six different species is associated with ribosomes. The patterns of ribosome protection are consistent with the translation of short peptides. lncRNAs show similar coding potential and sequence constraints than evolutionary young protein coding sequences, indicating that they play an important role in de novo protein evolution.
The study suggests that a lot of "noncoding" RNAs are being translated. The products appear to be short polypeptides of less than 100 residues.
New protein encoding genes do arise from time to time although the number of proven examples is very small. Let's assume, for the sake of argument, that a new gene arises about once every million years in a given lineage. That would mean about five new genes in humans since they split from chimpanzees and that seems about right for an upper limit.
Now, if you make a lot of junk RNAs by randomly transcribing junk DNA, then some of them will undoubtedly make short polypeptides. There's a chance that random mutations will create a peptide that takes on a functional role of some kind. There's an even smaller chance that this function will confer a selective advantage on the individual carrying the mutation. That's one way new genes are born.
Is this a reason for carrying a huge amount of junk DNA in your genome and making thousands of lncRNAs? Is the potential to make a new gene one million years in the future sufficient explanation for the preservation of junk DNA? The answer is "no."
You don't have junk DNA because it might proven useful in the future. You have it because you can't get rid of it. You don't transcribe your junk DNA because it might be useful, you transcribe it because the general properties of RNA polymerase and transcription factors don't allow for perfect discrimination between real genes and junk DNA. Junk transcripts aren't translated because they contain potential coding regions, they are sometimes translated because they must, by chance, contain some open reading frames.
Sloppiness might, by accident, lead to new genes but that's not why things are sloppy. If having junk DNA were a clear advantage for future evolution then the genomes of all extant lineages should have lots of junk DNA and should make lots of lncRNAs.
Ruiz-Orera, J., Messeguer, X., Subirana, J.A., and Alba, M.M. (2014) Long non-coding RNAs as a source of new peptides. eLife 2014;3:e03523 [doi: 10.7554/eLife.03523]
Many genes encode proteins and many other genes specify functional RNAs that do not encode proteins. The "RNA genes" include the classic genes for ribosomal RNAs and tRNAs as well as genes for very well-studied RNAs that carry out catalytic roles in the cell. There are a myriad of small RNAs required for things like splicing and regulation. All species, both prokaryotes and eukaryotes, contain genes for a wide variety or functional RNAs.
Eukaryotes seem to have an abundance of genes for small RNAs that perform a number of specific roles in regulation etc. They also have a lot of DNA regions complementary to long noncoding RNAs or lncRNAs (also lincRNA). The definition of long noncoding RNAs seems arbitrary and ambiguous [see Long Noncoding RNA]. Some of them might even encode proteins!
As a general rule, these RNAs are longer than 200 bp and some scientists put the cutoff at 1000 bp. Simple eukaryotes, such as yeast, don't have a lot of lncRNAs but eukaryotes with large complex genomes that are full of junk DNA seem to have a lot of different lncRNAs. The DNA regions1 that specify these lncRNAs ar not conserved. This strongly suggest that many of the lncRNAs are spurious nonfunctional transcripts even though some of them have well-characteized functions [see On the function of lincRNAs].
As usual, we have a definition problem. Are "lncRNAs" just a generic class of long noncoding RNAs that include thousands of nonfunctional molecules that are nothing more than junk RNA? Or, does the term "lncRNA" refer only to the subset that has a function? If it's the latter, then we should probably be referring to "putative" lncRNAs most of the time since the vast majority have not been shown to have a function. (There are about 10,000 of these RNAs in humans.)
I don't see how you can avoid the elephant in the room whenever you talk about lncRNAs. The most important question in NOT whether some of them have a function—that was demonstrated 30 years ago. The important question is whether the majority, or even a substantial minority, have a function.
That's why I was eager to read a short review by Rinn and Guttman in a recent issue of Science (Rinn and Guttman, 2014). They describe two lncRNAs that probably play a role in organizing chromatin within the nucleus (Xist and Neat1, both fram mammals). That's cool.
Then they say,
Collectively, these studies suggest that lncRNAs may shape nuclear organization by using the spatial proximity of their transcription locus as a means to target preexisting local neighborhoods. lncRNAs can in turn modify and reshape the organization of these local neighborhoods to establish new nuclear domains by interacting with various protein complexes, including chromatin regulators. Once established, a lncRNA can act to maintain these nuclear domains through active transcription and recruitment of interacting proteins to these domains. While the mechanism for how lncRNAs establish these domains is not fully understood, it is becoming increasingly clear that lncRNAs are important at all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization.
It sure sounds like they are describing a particular function (nuclear organization) to the majority of lncRNAs. But what if 90% of all 10,000 lncRNAs have no function and what if only 100 of the remaining functional lncRNAs are involved in nuclear organization? That means there are 900 functional lncRNAs that play a different role in the cell?
If that were true, you would write that last paragraph very differently. If you recognize the elephant, you might say something like this ....
Very few lncRNAs have been shown to have a function and there's a very good chance that most of them are spurious transcripts that have no function. However, a small percentage do seem to have a function. In this review we have identified some long noncoding RNAs that appear to be involved in nuclear organization. We propose to call these RNAs "noRNAs" for "nuclear organizer RNAs" on the grounds that once a function has been identified we should stop referring to them as lncRNAs.
But that doesn't sound nearly as exciting as the subtitle of the article, "Long noncoding RNAs may function as organizing factors that shape the cell nucleus" or the quotation that's prominently displayed in a box in the center of the page, "... it is becoming increasingly clear that IncRNAs are important in all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization." When did science become so dedicated to hype over substance? I must have missed the memo.
1. I use "DNA regions" instead of "genes" because the definition of a gene requires that the gene product be functional. You can't call them genes unless you have demonstrated that the RNA has a function.
Rinn, J. and Guttman, M. (2014) RNA and dynamic nuclear organization. Science 345"1240-1241 [doi: 10.1126/science.1252966]
The students in my third year lab course are about to test various food products to see if they contain any DNA from genetically modified organisms. They'll be using a variety of PCR primers to detect the Cauliflower mosaic virus 35S promoter and the nopaline synthase terminator sequence from the Ti plasmid of Agrobacterium tumefaciens [see Roundup Ready® Transgenic Plants ].
Every student has to bring in their own food sample to test but I'll be providing a number of "controls" that I picked up in the cafeteria and at the grocery store. Which ones are Frankenfood?
We're using some additional sets of primers as controls. One set detects a chloroplast gene (rbcL). We have two sets of primers for corn-specific genes (invertase and zein) and one set for a soybean specific gene (lectin). An important part of the exercise is figuring out what controls to use and what DNA samples to analyze. Each group of two students can do 24 PCR reactions. It's going to be a challenge for them to figure out which reactions are the most important.
(They were told that corn and soy products are most likely to test positive in the GMO assay.)
Barry Arrington is a lawyer from Colorado [Encyclopedia of American Loons]. Here's an example of the logic of lawyers posted on Uncommon Descent [Not Merely False].
The following statements are so obvious as to be considered truisms.
1. The primordial datum: I am subjectively self-aware.
2. It is not possible even in principle to account for mental facts, such as the primordial datum, on the basis of physical facts. They are different sorts of things; therefore one cannot account for the other. Trying to account for subjective self-awareness by suggesting it is an epiphenomenon of the electro-chemical process of the brain is like saying the color blue can be reduced to its constituent banana peels.
3. It follows that a reductionist materialism is not merely false but obviously false.
4. Just as obviously, it does not follow that committed materialists will admit that reductionist materialism is false, for they have reasons to put their faith in their metaphysical commitments that have nothing to do with the evidence and logic of the matter.
I would not want him to defend me if I were innocent. On the other hand, he might be a good choice if I were guilty because I could easily fool him into thinking that I was innocent.
Maud Menten is best known for the Michaelis-Menten equation and her work on enzyme kinetics. She was born in Port Lambton, Ontario and she is a graduate of the University of Toronto.
The "mystery" concerns her degrees and the year she graduated. The video below was prepared when she was inducted into the Canadian Medical Hall of Fame in 1998 [Maud Menten]. If you watch the first few minutes you'll hear that in 1911 Maud Menten was one of the first Canadian women to receive a medical degree. You find similar statements all over the web, although sometimes it says she graduated in 1913—as in the text on the Canadian Hall of Fame website.
Most people don't understand the consequences of genetic testing. You may think that you can handle all of the data and information but think again.
This is the story of someone who got their DNA tested by a commercial company and he persuaded his parents to participate as well. What could possibly go wrong? The title of the article tells the story: With genetic testing, I gave my parents the gift of divorce.
Turns out he has a half-brother! His father never mentioned that he had a son with another woman.
At first, I was thinking this is the coolest genetics story, my own personal genetics story. I wasn't particularly upset about it initially, until the rest of the family found out. Their reaction was different. Years of repressed memories and emotions uncorked and resulted in tumultuous times that have torn my nuclear family apart. My parents divorced. No one is talking to my dad. We're not anywhere close to being healed yet and I don't know how long it will take to put the pieces back together.
It's not always true that having information is better than not having information. If you beleive that then you are very naive.
Do Intelligent Design Creationists (IDiots) understand evolution? ... of course not.
It's been really frustrating over the past 25 years trying to explain modern evolutionary theory to IDiots. They continue to refer to "Darwinism" and "neo-Darwinism" but it's obvious that they don't have a clue what they mean by those terms. This become especially obvious when they discover, once again, that real evolutionary biologists don't accept the IDiots' version of evolutionary theory.
Check out the latest post by Casey Luskin on Evolution News & Views. It would be so easy for him to explain to his readers what the textbooks say on evolutionary theory and how it differs from what the IDiots are promoting in their own books and on their websites [Are Biologists Rejecting Neo-Darwinian Evolution?]. He doesn't do this, of course, and that's only partly because it suits his purpose to be dissembling. It's mostly because he really doesn't understand what he's talking about. We know this because dozens of people have tried to explain it to him over the years and he still doesn't get it.
In fairness, Casey Luskin is responding to an article on The BioLogos Forum by philosopher Robert C. Bishop [Two Rhetorical Strategies (Reviewing “Darwin’s Doubt”: Robert Bishop, Part 2)]. It's pretty clear that Bishop doesn't understand modern evolutionary theory either. Unfortunately, there are many scientists who share these misconceptions but that's not an excuse for Luskin and his fellow travelers since they are supposed to understand what they spend so much time attacking.
I'm usually a big fan of Jesus and Mo but today's cartoon is a bit disappointing. It is "resurrected" from 2009 [nerve2] and it is prompted by an excellent article on militant atheists written by Nick Cohen [The phantom menace of militant atheism]. Even Jerry Coyne likes it [A wonderful attack on the "militant fundamentalist atheism" trope].
The issue here is whether an atheist needs to study all religions in order to be an atheist. The barmaid seems to concede that point since she advances arguments that require knowledge of specific religions. Both of her examples require the provisional acceptance of gods because they refer to particular properties of those gods (i.e. whether they can have sons and prophets).
A Christian, for example, would happily engage the barmaid in a debate about the the divinity of Jesus as long as they begin with the assumption that gods exist. In order to engage seriously in that debate, the barmaid would have to read a ton of Christian apologetic literature. In other words, she would have to understand "sophisticated" religion. She would not be defending atheism even if she won the debate since there are billions of religious people who don't believe in the divinity of Jesus.
But atheists, by definition, don't believe in gods. The only arguments that are relevant are whether gods exist. Those arguments are not specific to any particular religion and they certainly aren't going to be found in the Bible or the Qur'an. I do not accept the premise that gods exist so I'm not the least bit interested in studying the religious beliefs of anyone who begins with the "fact" that gods exist. I'm about as interested in debating whether any of the gods had children as I am in debating how many angels can dance on the head of a pin.1
The atheist barmaid made a mistake. She should have said "Let's see - I understand that all religions begin with the idea that gods exist. What evidence do you have that this is true?"
Or, for that matter, the problem of evil. If there are no gods then there's no problem. Debating the "problem" of evil or whether Jesus is the son of gods is just like debating the cut of the Emperor's new clothes [On the Existence of God and the Courtier's Reply].
Today's the day that clubs strut their stuff and try to get new students to sign up. It's an important part of campus life and an important part of a university education even though the majority of students don't participate.
There's a club for just about everyone, even biochemists!
All of that will disappear when universities shut down and undergraduate education is confined to MOOCs and glorified Skype conferences. You can't join a rowing club if you're a thousand kilometers from the clubhouse.
I suppose there are lot of business types out there who don't care about this sort of thing as long as you pay your money, get a degree, and go on to a decent job where you can pay back your student loan.
It's hilarious even when you know it's photoshopped.
This month's issue of The Atlantic has another one of those boring articles on the imminent death of universities (colleges) [The Future of College?].
This time it's a new "university" called MINERVA that's going to kill off all the old-school schools. Minerva is a for-profit university where all the learning takes place in electronic seminars of up to 19 students. Sort of like a Skype conference call only it uses copyrighted software. Students will pay only $28,000 (US) per year for this experience.
There have been articles about the death of universities published every year for as long as I can remember. Almost all of them think that a "university" is just a place where you go to get an undergraduate education. That's because almost all of the potential murderers only experienced university as an undergraduate.
Apparently the Queen's Guards surprised everyone by playing a new song during the changing of the guard at Buckingham Palace on July 15, 2014.
Name that song!
Do you know it?
Here's a hint ... the actual theme is better but it's the thought that counts.
The Economist has surveyed cities from all over the world to find the ones that are the most livable (i.e. best places to live). Here's a summary of the criteria described in the report [A Summary of the Liveability Ranking and Overview]
The concept of liveability is simple: it assesses which locations around the world provide the best or the worst living conditions. Assessing liveability has a broad range of uses, from benchmarking perceptions of development levels to assigning hardship allowance as part of expatriate relocation packages. The Economist Intelligence Unit’s liveability rating quantifies the challenges that might be presented to an individual’s lifestyle in any given location, and allows for direct comparison between locations.
Bjørn Østman alerted me to the list by posting a link to this article: The World's Most Livable Cities All Have One Big Thing in Common. What do the top ten cities all have in common?—none of them are in the USA.
Here's the list ....
1. Melbourne, Australia
2. Vienna, Austria
3. Vancouver, Canada
4. Toronto, Canada
5 (tie). Adelaide, Australia
5 (tie). Calgary, Canada
7. Sydney, Australia
8. Helsinki, Finland
9. Perth, Australia
10. Auckland, New Zealand
There's obviously more to "livability" than meets the eye. Some of these places are a lot less interesting than Paris, London, or New York.
I think the ranking also depends very much on how much money you have. I'd need to be offered a hell of a lot more money if I were to consider a move to Calgary, Helsinki, or Perth.1
1. I've never been to Perth but it doesn't seem like a place I'd like to live.
Modern evolutionary theory is far more advanced than the simple version that's attacked by Intelligent Design Creationists. Neutral Theory, population genetics, and the importance of random genetic drift are just a few of the additions that were incorporated in the 1960s. (That's almost 50 years ago.)
Most IDiots are half-a-century behind in their knowledge of science. They think that random mutations and natural selection are the only way that evolution can occur.1 That's why they refer to evolution as "Darwinism."
Many of them have heard vague rumors of change, proving that from time to time they do, indeed, take their fingers out of their ears. They've discovered that modern scientists have moved well beyond natural selection as an explanation for every bit of evolution. This makes the IDiots very happy since, to them, it means that evolution is wrong. And if evolution is wrong then gods must exist.
They've even developed a course to explain why Neutral Theory and random genetic drift support the idea that gods must be making bacterial flagella and protein-protein contacts. It looks like a very interesting course ...
PZ Myers [Oh, dear] picked up on a tweet from Jeffrey Ros-Ibarra [Tell me botany doesn’t have a recruitment problem]. He posted the result of a survey of 800 first year students.
This shouldn't come as a big surprise to any Sandwalk readers. The question is, what should we do about it?
Most university professors share this bias so they are very comfortable with teaching biochemistry from a strictly animal (mostly human) perspective. When challenged, they point out that students are mostly interested in animals and themselves. They think we should design our courses to accommodate these interests because that's what students want to hear. I call these professors the "caterers."
A minority (that includes me) look upon this data as a challenge. Our goal is to convince students that they should broaden their interests and learn about other species. People like me will emphasize broad principles and concepts that apply to ALL living organisms. We teach comparative biochemistry and talk a lot about evolution. These guys are the "challengers." (They're also the ones with the low student evaluations.)
The easiest way to tell the difference between the two types of professor in introductory biochemistry courses is to see whether they teach photosynthesis or the glyoxylate shunt, and whether they spend as much time on gluconeogenesis (the most ancient pathway) as they do on glycolysis (the derived pathway). It's also informative to observe whether they cover the biosynthesis of amino acids or whether they treat amino acids as food.
It's a really bad sign if they spend any time at all on the difference between "essential" and "nonessential" amino acids.
There aren't very many big questions left to answer. Most ot the great debates have been settled and we're now in a mopping up situation.
One of the few remaining questions concerns the function of IDiots. The Intelligent Design Creationist Movement has been a spectacular failure. The Wedge Document is a joke. They've failed to get creationism into American schools. People are abandoning Christianity. Their books have all been trashed by critics.
One wonders why they're still around. They must be thinking the same thing because David Klinghoffer has put up a recent post on this very issue [You're Welcome: Darwinists Should Thank Us for Quality Control, Fact-Checking]. It turns out that the function of IDiots is to keep real scientists honest by finding flaws in their reasoning and errors of fact.
Casey [Luskin] points out that in any marketplace—whether vendors are promoting consumer products or ideas about evolution—competition improves the products and the service. The absence of competition almost always results in shoddy products and poor consumer service, as anyone who has visited a socialist country can tell you. Darwin advocates should be thanking us.
Of course the flipside to all this is that for every orthodox evolutionist who is made more judicious and truthful in what he argues, there's probably another who prevaricates about the meaning of scientific data, because "What will the creationists say?"
Still, on the whole, they and everyone else who cares about getting at the truth in science ought to be glad we're here.
Who knew?
From British embassy apologizes for cheeky tweet commemorating White House burning.
... in what some considered a cheeky jab, the Washington wing of the British embassy came under fire from some unimpressed Americans for its commemoration tweet. On Aug. 24, 1814, British troops invaded Washington, D.C., setting the White House on fire during the War of 1812. The attack was in response to an American attack on the city of York (present-day Toronto).
The tweet featured a photo of a sheet cake adorned with a miniature White House with the respective countries' flags on each side.
"Only sparklers this time," the embassy wrote to cap off the tweet.
The blogosphere is excited about a petition that's being presented to the Scottish Parliament on behalf of the Scottish Secular Society. A chemist, and Nobel Laureate, Sir Harold Kroto, has backed the petition [Nobel prize winner backs Scottish Secular Society petition to exclude creationism in Scottish schools].
Here's what it says ....
Calling on the Scottish Parliament to urge the Scottish Government to issue official guidance to bar the presentation in Scottish publicly funded schools of separate creation and of Young Earth doctrines as viable alternatives to the established science of evolution, common descent, and deep time.
I would never, ever, sign such a petition. I think it's a bad idea for politicians to get involved in the specifics of what should and should not be taught in publicly funded schools. You can see what happens in the USA when you give them that right.
If the teaching of Young Earth Creationism is creeping into Scottish schools then it's time to show students why it is wrong and why science can refute it. Banning it will only make it seem like a genuine threat that can't be confronted by teachers and education.
John Wilkins tries to show that philosophy is not a waste of time. He describes philosophers who are anti-realists and wonders whether genes actually exist.
The IDiots are claiming to have "predicted" something that's been known for thirty years.
Let's start by reviewing some basic facts about codons.
Look at the standard genetic code (right). Notice that for some amino acids there are several codons. For example, There are four different codons for alanine (A): GCT (GCU), GCC, GCA, and GCG. These are called "synonymous" codons.
A lot of mutations in coding regions will change one codon into another without changing the amino acid encoded by the mRNA. These are presumably neutral mutations, since they occur frequently in populations and in comparisons between species. What this means is that it mostly doesn't matter which codons are being used.
We all know the drill by now. Intelligent design Creationists attempt to discredit evolution and science by pointing out what they see as flaws in basic theory. They also spend a considerable amount of time attempting to discredit individual scientists using guilt by association or direct character assaults.
One of their favorite tricks is to lift quotations out of context and present them in a way that makes it look like famous scientists are supporting Intelligent Design Creationism—or, at least, supporting the idea that evolution is flawed.
The tactic is so widespread and despicable that it led to formation of The Quote Mine Project
Or, Lies, Damned Lies and Quote Mines. That project ran out of steam about eight years ago because the authors just couldn't keep up with all the misinformation coming out of books, lectures, and articles from leading members of the Discovery Institute.
Stephen Meyer is a expert at this. Here are a couple of examples from his book Darwin's Doubt (2013).
Michael Behe has tried to explain where I'm going wrong and why evolution is highly improbable [Guide of the Perplexed: A Quick Reprise of The Edge of Evolution]. He lists a number of bullet points that are supposed to explain his argument. Let's look at each one ...
- If the development of some particular adaptive biochemical feature requires more than one specific mutation to an organism's genome, and if the intermediate mutations are deleterious (and to a lesser extent even if they are neutral), then the probability of the multiple mutations randomly arising in a population and co-existing in a single individual so as to confer the adaptation will be many orders of magnitude less than for cases in which a single mutation is required.
This is correct. The probability of any single mutation occurring is equal to the mutation rare, which is about 10-10. The probability of an additional specific mutation occurring is also 10-10. The combined probability of any two specific mutations occurring is 10-20.
In spite of what they say, the Intelligent Design Creationist movement is primarily an anti-science, anti-evolution movement. Something like 99% of their efforts and activities are directed toward discrediting scientists and science. The 1% of their effort devoted to promoting scientific evidence for creationism has been a spectacular failure.
Here's a new video produced by John G. West. In case you don't know who John G. West is, here's what Wikipedia [John G. West] says about him ...
John G. West is a Senior Fellow at the Seattle-based Discovery Institute (DI), and Associate Director and Vice President for Public Policy and Legal Affairs of its Center for Science and Culture (CSC), which serves as the main hub of the Intelligent design movement.
The video was posted to YouTube on Aug. 14, 2014 and it is copyrighted by the Discovery Institute. I learned about the video from a post on Evolution News & Views (sic) [Coming to Grips with the Truth About Social Darwinism].
The video has nothing to do with evolution and evolutionary theory but IDiots believe that it does. That's, of course, why we call them IDiots.
One of the most fascinating things about philosophy is the fact that philosophers still can't agree on the major issues even after debating them for hundreds of years. For example, they still can't, as a discipline, agree on whether there are good arguments for the existence of gods. Many universities have theologians who masquerade as philosophers and publish in philosophy journals.
Philosophers are still discussing the mind-body problem. In other words, there actually are legitimate philosophers who call themselves dualists and think that the mind is something more than the workings of matter. Some philosophers think there are moral absolutes while others are ethical relativists and some are something else. Apparently, several hundred years of debate hasn't resolved this issue either.
Recently (last century) the discipline of philosophy has spun off a subdiscipline known as the "History and Philosophy of Science." This is now a separate department in many universities.
I got curious about student debt when I saw a YouTube presentation about the "squeeze generation." The point of the talk was to explain how difficult life is for the under 45 group compared to their baby boomer parents.
The video repeated the common claim that average student debt was about $23,000. I've always been puzzled by this claim since most of my friends were able to help their children get a university education just as our parents helped us. Most of our children were able to graduate from university (undergraduate degree) with no debt.
If about half the graduating class got help from their parents, as we did, then the average debt of those students with debt must be about $46,000 and that's unreasonable.
I was a little bored yesterday so I watched God's Not Dead.
There's good news and bad news.
The bad news is that I wasted almost two hours.
The good news is that if this is the best Christians can do then rational people are not threatened. On the other hand, unbalanced people—like the Christians in this mover—can be unpredictable, so maybe we should be worried.
The most repulsive scene is when a Christian pastor tries to force a dying atheist (car accident) to accept Jesus. The second most repulsive scene is when the hero's Christian girl friend leaves him because he wants to stand up for his faith. If those people are typical Christians then it's no wonder that people are abandoning Christianity.
Let me say, right from the beginning, that Michael Behe's book The Edge of Evolution is very interesting and provocative. Many of my colleagues think that Behe's main argument can be easily dismissed as the work of an uninformed IDiot who is blinded by his religion. There's some truth in that, but only a little.
The main thesis of the book is that there are some combinations of mutations that could theoretically be beyond the reach of evolution during the 3 billion years that life has evolved on Earth. Behe refers to this combination as a double CCC (1040). It's his estimate of the probability of a particular combination of four specific mutations arising by chance. Since we know that such combinations have arisen, Behe concludes that god(s) must have been involved.
There are many ways of exploring Behe's calculations in order to see if he has a point. The first problem is that the meaning of his conclusion is very unclear. Let's think about it this way ...
Apparently I flunked the Behe challenge [Laurence Moran's Sandwalk Evolves Chloroquine Resistance]. Let's review what happened.
In his book, The Edge of Evolution, Michael Behe calculated the odds of a malaria parasite developing resistance to chlorquine by assuming that two separate mutations were necessary. Here's what he said on page 57 ...
How much more difficult is it for malaria to develop resistance to chloroquine than to some other drugs? We can get a good handle on the answer by reversing the logic and counting up the number of malarial cells needed to find one that is immune to the drug. For instance, in the case of atovaquone, a clinical study showed that about one in a trillion cells had spontaneous resistance. In another experiment, it was shown that a single amino acid change at position number 268 in a single protein, was enough to make P. falciparum resistant to the drug. Se we can deduce that the odds of getting that single mutation are roughly one in a trillion.
The debate over the existence of human races has heated up recently with the publication of a book by science writer Nicholas Wade. The book is ridiculous, by all accounts (I haven't read it). In fact, it is so wrong that a group of geneticists have written an open letter refuting the claims [see Geneticists decry book on race and evolution].
There are several aspects of this controversy that interest me greatly. One of them has to do with the reputation of science writers. Nicholas Wade was a science writer for Nature (1967-1971), Science (1972-1982), and the New York Times (1982-2012). I've often heard heard him being referred to as one of the best science writers, particularly by other science writers. That's an opinion that I've never shared and I'm glad to see him get his comeuppance.
Science writers aren't doing so well these days.
Micheal Behe came to Toronto a few years ago and gave three talks on the campus of the University of Toronto. One of them was in the big lecture hall in my building (Medical Science Building). I went to all three lectures and enjoyed them immensely even though I disagreed with what he was saying [Michael Behe in Toronto: "What Are the Limits of Darwinism?"] [Michael Behe in Toronto: "Evidence of Design from Biology" ]. It was fun meeting him again and talking to him about his views. You can learn a lot about what people think by attending a lecture and seeing how they respond to questions and debate.
That's what a university is all about. I also greatly enjoyed a lecture by William Dembski a few years ago. I got to meet him and I got to ask a question at his lecture. It was a very valuable experience. Over the years I've heard several creationists speak on my campus, even Hugh Ross. Attending those lectures has put me in touch with many creationist sympathizers in my area and I've formed a number of friendships. Some of them read my blog.
Vincent Joseph Torley (vjtorley) has several degrees listed on his website. Quoting ...
- Bachelor of Science, completed in 1981, at the Australian National University, Canberra. Major: Pure Mathematics. Other subjects studied: Physics (2 years), Chemistry (2 years), Geology (1 year) and Science German (1 year).
- Bachelor of Arts, completed in 1986, at the Australian National University, Canberra. Majors: Philosophy and Computing Science.
- Bachelor of Economics, completed in 1987, at the Australian National University, Canberra. Majors: Economics and Accounting. Other subjects studied: Statistics (2 years).
- Master of Arts in Philosophy, completed in 1994, at the University of Melbourne, Australia. Thesis topic: Laws of Nature (Scientific Laws). Grade: 2A.
- Ph.D. in philosophy, which I received in August 2007 from the University of Melbourne, Australia. Thesis topic: The Anatomy of a Minimal Mind.
.... end quote.
He hasn't studied much biology and his undergraduate science degree, obtained 26 years ago, was a major in pure mathematics.
That hasn't prevented him from writing extensively about biology and evolution. His latest contribution is a critique of Keith Blanchard's article on Why you should stop believing in evolution: You don't believe in it — you either understand it or you don't. That article has attracted attention from evolution supporters who think he got some things wrong [see Glenn Bransch's Five Quibbles for Blanchard]. I agree with them. Blanchard does not present the best case for evolution and he seems to lack a deep understanding of evolution.
Vince Torley's article is worth reading because it illustrates some of the confusions in the minds of IDiots as they struggle to catch up with 21st century biology [see Why Keith Blanchard really doesn’t understand evolution]. However, that's not the point I want to make today. Instead, I want to quote a paragraph from near the end of Vincent Torley's article ....
I could go on, but I’d like to conclude this article with a final observation: Keith Blanchard doesn’t have a science degree. His LinkedIn profile lists him as having a two year tech degree in Electronic Technology, which he obtained in 1975. Let us freely grant that the man’s skill set looks quite impressive. Nevertheless, the fact remains that a man without a science degree has no place writing an article on evolution in a popular online magazine like The Week. It’s simply presumptuous.
I wonder if there are any prominent Intelligent Design Creationists who don't have real science degrees?
I love watching "Who Do You Think You Are." The latest episode features Rachel McAdams and her sister Kayleen who search for their Canadian ancestors. They discover a family who settled on the shores of Lake Champlain in the mid-1700s and got caught up in the Revolutionary War. Their ancestors supported the government (Great Britain) against the revolutionaries and when General Burgoyne's invasion from Canada was stopped at the Battles of Saratoga (1777) the loyalists had to flee to Canada with the retreating army.
The McAdams ancestors spent a year or so at a refugee camp near St. Johns in Quebec, near the American border. The sisters visit the site during the show. It looks like one of the young sons of their ancestors died during the stay in the refugee camp—probably because the conditions were pretty horrible.
One of my ancestral families was Isaac Montras and his wife Tamar Betts. They had a farm near Saratoga and they supported the British side during the revolution. They also had to leave their farm and flee to Canada after the Battles of Saragota. They were settled at another refugee camp in Machiche, Quebec where they stayed for a year before moving on to settle in Nova Scotia.
Tens of thousands of United Empire Loyalists came to Canada after the Thirteen Colonies gained their independence from Great Britain. Nobody knows how many of the residents of the Thirteen Colonies remained loyal to the government in Great Britain but it may have been as much as one-third of the total population. Only a small percentage of them left after the war was over.
You can watch a clip from "Who Do You Think You Are" featuring the McAdams sisters at: Rachel McAdams Learns Her Ancestors' Loyalties. If you want to watch an entire show, I recommend the British version that's been around for ten seasons. Here's one on J.K. Rowling.
Michael Behe is at it again. He has a freaky knack of taking scientific results that directly contradict his views and twisting them into confirmation that only god can explain the result.
This time he is revisiting an old issue. Joe Thornton's lab has published a series of papers showing that the evolution of the glucocorticoid receptor involved a number of neutral steps that were absolutely required before the receptor could acquire the ability to bind to cortisol. Each of the steps was contingent on earlier steps. This is evolution by accident.
This conflicts with Michael Behe's view of evolution because he maintains that there's an edge of evolution defined by pathways that involve multiple steps. According to Behe, all the multiple mutations have to take place at the same time because none of the intermediates are beneficial and most of them are detrimental.
I visited the Institute for Creation Research back in 1992 when it was still based in Santee, California (USA). I toured the museum and bought this wonderful poster in the gift shop. It now hangs on the wall outside my office. I relate to the pirates.
A much simpler black and white version (below) was shown to a high school class in Atlanta, Georgia, USA and it caused quite a stir [Flap over creationist cartoon shown in high-school class]. I can understand why. The color poster that I bought twenty years ago is much better. I can see why the Atlanta high school students weren't impressed with the pirates.
Seriously, I don't think evolution supporters should make a fuss about this [see Evolution vs. creationism: Does this cartoon belong in Grady High School biology class? ]. It may provide some comfort to the diehard fundamentalist Christian students in the class but lots of students are going to make fun of the cartoon and that may have a beneficial effect in the long run. We should be careful about putting up obstacles that prevent creationists from shooting themselves in the foot.
(I know about the so-called "separation of church and state" provision in the American Constitution. You don't need to lecture me on the legality of showing a religious cartoon in a public high school.)
Drugmonkey (@drugmonkeyblog) doesn't think there's a filter problem [There is no "filter problem" in science].
He writes,
Seriously.
It is your job as a scientist to read the literature, keep abreast of findings of interest and integrate this knowledge with your own work.
We have amazing tools for doing so that were not available in times past, everything gets fantastically better all the time.
If you are a PI you even have minions to help you! And colleagues! And manuscripts and grants to review which catch you up.
So I ask you, people who spout off about the "filter" problem.....
What IS the nature of this problem? How does it affect your working day?
I'm trying to keep up with a number of very broad and diverse fields. For example, as a textbook author, I need to keep abreast of just about everything that might be covered in an introductory biochemistry course. I'm also trying to keep informed about evolutionary biology; especially molecular evolution because I teach a course on that topic and I blog about it. I don't want to miss exciting developments in pedagogy (teaching) and the philosophy of science. Finally, I like to be up-to-date on the latest advances in other disciplines.
Here's the problem. There's a lot of junk out there. It's a waste of time to scan all of the science journals that might possibly have something of interest to me and it's a waste of time to get any "tools" to do it for me. Most of the time I wouldn't even know what to ask for. For example, I don't want to see all the papers on photosynthesis but I need to see the one that's going to change my textbook. I don't want to see all the papers on mutation rates but I do want to see the ones that are worth blogging about.
There were times when I could sit down for a few hours every week and scan the tables of contents of the leading journals in my field. Those days are long gone and my "field" has expanded enormously. I need to filter but I'm pretty sure I'm missing some important papers. In fact, I know this because just about every month I hear from others about things that I've missed months, or even years, ago.
I have a filter problem. I'm filtering out some important things and reading far too much junk. My filter problem can't be solved. If it wasn't for blogs, I'd be in bigger trouble.
We're in the middle of a discussion about the function wars. It's obvious to me that members of the ENCODE Consortium also have a filter problem. They've filtered out all kinds of information about the organization of the human genome. They don't understand the evidence for junk DNA, for example, and they don't have a good grasp of evolution. On the other hand, they've probably read every recent paper on the methodology of RNA-Seq, ChIP, and data analysis algorithms.
I'm glad that drugmonkey doesn't have a filter problem. Or, should I say, I'm glad that he THINKS he doesn't have a filter problem. It must be comforting to believe that he's keeping abreast of everything relating to his interests. I've never felt like that.
The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.
Stephan Jay Gould (1982)This is my fourth post on the function wars.
The first post in this series covered the various definitions of "function" [Quibbling about the meaning of the word "function"]. In the second post I tried to create a working definition of "function" and I discussed whether active transposons count as functional regions of the genome or junk [The Function Wars: Part II]. I claim that junk DNA is DNA that is nonfunctional and it can be deleted from the genome of an organism without affecting its survival, or the survival of its descendants.
In the third post I discussed a paper by Rands et al. (2014) presenting evidence that about 8% of the human genome is conserved [The Function Wars: Part III]. This is important since many workers equate sequence conservation with function. It suggests that only 8% of our genome is functional and the rest is junk. The paper is confusing and I'm still not sure what they did in spite of the fact that the lead author (Chris Rands) helped us out in the comments. I don't know what level of sequence similarity they counted as "constrained." (Was it something like 35% identity over 100 bp?)
My position if is that there's no simple definition of function but sequence conservation is a good proxy. It's theoretically possible to have selection for functional bulk DNA that doesn't depend on sequence but, so far, there are no believable hypothesis that make the case. It is wrong to arbitrarily DEFINE function in terms of selection (for sequence) because that rules out all bulk DNA hypotheses by fiat and that's not a good way to do science.
So, if the Rands et al. results hold up, it looks like more that 90% of our genome is junk.
Let's see how a typical science writer deals with these issues. The article I'm selecting is from Nature. It was published online yesterday (Aug. 6, 2014) (Woolston, 2014). The author is Chris Woolston, a freelance writer with a biology background. Keep in mind that it was Nature that started the modern functions wars by falling hook-line-and-sinker for the ENCODE publicity hype. As far as I know, the senior editors have not admitted that they, and their reviewers, were duped.
On most days I'm an optimist. I think that eventually the truth will win out and all you have to do is convince people that they are misguided. That's why I spend so much time discussing the view of Intelligent Design Creationists. On the good days, I firmly believe that if I can show them what science is all about then they will come around to accepting evolution.
I cherish a few modest successes over the years. For example, a few months ago I tried to teach David Klinghoffer and his friends about modern concepts of evolution and genetics. The example I used was the 98% sequence similarity between the human and chimp genomes. I showed him that the similarity is quite consistent with our understanding of Neutral Theory and random genetic drift [Why are the human and chimpanzee/bonobo genomes so similar?].
A remarkable thing happened. Some of the Intelligent Design Creationists on Evolution News & Views (sic) and Uncommon Descent actually agreed with me! They tried to explain to their fanatical friends that chimps and humans really do share a common ancestor and that the differences between them are explained by evolutionary theory. (I've included links to all the posts at the bottom of this post.)
Just when you think you are making some progress, the IDiots prove you wrong. Yesterday on Uncommom Descent there was a post on the topic of the similarity between chimps and humans [At last, a proposed answer re 98% human-chimpanzee similarity claim]. The author was probably Barry Arrington posting as "News." Here's the relevant part of that post ...
From this comment (by Gordon Davisson, in response to this post):
In other words, I’m agreeing with Denyse here:
BUT claimed 98% similarity due to a common ancestor (a claim that hundreds of science writers regularly make, in support of common descent) *undermines anything else they have to say on the subject.*
I do not know how to put the matter more simply than this: A person who does not see the problem is not a credible source of information.
He responds:
…just disagreeing about which side is not credible. Take the 98% similarity figure as an example: one of the basic principles of science is that you must follow the evidence. If the evidence supports the 98% figure, and that conflicts with your intuition, then you either have to throw that intuition into the trash bin, or stop claiming to be doing science.
No. Absolutely not.
One should never discard intuitions formed from experience, especially about vast claims. Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science.
This is called, among other things, wanting to have your cake an eat it too. The IDiots want you to believe that they accept all of modern science and that their "theory" is consistent with the evidence.
On the other hand, if the science of genetics leads to conclusions that contradict your "intuition" then the science must be wrong.
We've known for decades that this is how the IDiots really think but it's interesting to see someone like Barry Arrington express it so openly.
Now all we have to do is sit back and wait for the more intelligent IDiots to point out that we've been through all that a few months ago and Barry's intuition is wrong. Instead, what we're seeing is Barry Arrington doubling down [Sun orbits Earth vs. Chimps are people too – the differences].
This is not a good day. It's hard for me to remain optimistic.
An Intelligent Design Creationist explains why chimpanzees and humans are so similar
IDiots respond to the evidence for evolution of chimpanzees and humans
A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory
Breaking news: Creationist Vincent Torley lies and moves goalposts
Vincent Torley apologizes and claims that he is not a liar
Vincent Torley tries to understand fixation
On the frustration of trying to educate IDiots
Why creationists think they are more open-minded than scientists
What would happen if Intelligent Design Creationists understood evolution?
Branko Kozulic has questions about fixation
Branko Kozulic responds
Branko Kozulic responds: Part II
