Pun four

Pun three

Pun two

Pun one

Problems with My Citations

Google Scholar Citations is not quite working the way I had expected. Apparently I am the author of a 1935 paper on Field of Science in the journal Women. I wish.



Title: Field of Science
Authors: Bjørn Østman
Publication date: 1935/2
Journal name: Women
Volume: 2009
Pages: 432
Description:
Why drug design is like airplane design. And why it isn't. ... Influenza - putting the Trojan into the horse but should you open it? ... ResearchBlogging.org When the environment is stable, it's good to be robust against mutations. This is because all mutations in an adapted organism will be deleterious or neutral. ... When the environment changes, being robust against mutations means that it is more difficult to adapt, so being robust is not good. This is because robust organisms have a hard time finding the mutations that lead to phenotypic change.

Don't panic! CoE #42 is here

In case you missed it, The Hitchhiker's Guide to Evolution (aka CoE #42) is up at the Ocelloid.


Image created by Troy Britain.

The Muslim creationists refuse proper education

A second wave of creationists are making trouble, following Christian creationists (who are not done, but seems to be get less media attention these days). Muslim creationists are now walking out of medical lectures because of their beliefs.

Muslim students, including trainee doctors on one of Britain's leading medical courses, are walking out of lectures on evolution claiming it conflicts with creationist ideas established in the Koran.

Would you want to be treated by a physician who skipped classes that mentioned evolution? Microbes that make us sick evolve fast, leading to antibiotic resistance and virulence. Humans have many traits that are shaped by evolution, and the genetic differences among different ethnicities is likewise a subject of evolution. Should we not require that medical doctors know about these topics? Imagine if you weren't sure if your doctor knew enough about some disease because he had walked out on all lectures that mentioned Darwin or evolution. No thanks for me. [Evolutionary medicine.]

The emergence of the schism between Islam and evolution has much to do with Adnan Oktar (aka Harun Yahya). I have written about him before:
Stasis does not falsify evolution
Adnan Oktar repeats challenge ($$$) in a white suit
Creationism in Europe is also bad

Suffice to say that he is the author of the Atlas of Creation, a lush illustrated tome of fishing lures sent free of charge to academics in much of Europe and the US.

As stupid as Christian creationists have proven to be, I fear that will be nothing compared to the zealotry of their Muslim counterparts.

Reproductive species vs. ecological species

Why are two breeds of dogs who can't mate without human assistance the same species, while two fish species, which can and do have fertile offspring, but which are intermediate in size and therefore not as good at obtaining resources as the parents, are different species?


The dog example is pre-zygotic isolation, and would seem prohibitive, if not for human assistance. The fish example is called "extrinsic post-zygotic isolation". So, we have that we consider populations who can't actually interbreed the same species, but those who really do mate are different species.

Personally, I can go either way (but do have a preference), but I really wish we could all agree to apply the Biological Species Concept a little more rigorously. My point is always that the BSC doesn't always work (as with (mostly) asexual species, such as bacteria), and other definitions should then be used. My view is that if two populations are different species by any of a set of good species definitions, then they should be called different species. This is an all-encompassing view of what species are.

Don't lose track of the fact that what we are trying to do when we designate something as species is to say something about biology. At the end of the day, species is a term that must say something about the clustering of genomes, and remember that it is possible to cluster a continuum.

Other good species definitions include the Ecological Species Concept, which classifies species as a set of organisms adapted to a particular set of resources, called a niche, in the environment. This definition* is more difficult to test for in natural populations, but that is neither here nor there when we talk about these basic theoretical questions.

And do note that here I am not even talking about the appropriateness of applying one definition when it doesn't match the actual process by which speciation occurred. Two populations may diverge and become different ecological species despite continuous interbreeding, and only after many generations become reproductively isolated (as in not able to have fertile offspring, for whatever reason, save physical isolation). Thus, saying that there are only different species many generations hence when some mutation occurs that changes the ability of sperm to enter the egg, say, makes no sense in the light of the adaptive processes that made the two groups different.

Let's call two populations different "reproductive" species or "ecological" species when the BSC or the ESC applies, and let's for Heaven's sake be rigorous when applying them!

P.S. If you want to have a crack at this, please don't think you can resolve this by putting meaning into the use of the words "breeds" and "species" in the examples above, 'kay?

* Oh why oh why must we call the definitions "concepts"? A "species" is a concept. Tsk, tsk, Mayr.

Reference:

Rice, W., & Hostert, E. (1993). Laboratory Experiments on Speciation: What Have We Learned in 40 Years? Evolution, 47 (6) DOI: 10.2307/2410209

Who benefits from giving advice about résumé writing?

Interesting little commentary on how (not) to do a résumé: Final Cut: Words to Strike from Your Resume.

I don't have a résumé, 'cause in science that isn't expected. I have a CV, and the difference is that there we just list pretty much everything we've ever done, as opposed to write about how great we are. But I used to have one when I was working as a programmer, and I made just the mistakes that Elizabeth Lowman cautions against:

• Saying what you hope to do in your next job (you should list your top accomplishments)
• Saying you're experienced (you should give details of that experience)
• Saying you're a team-player (you should give examples of how you have been a successful team-player)
• Saying you're dynamic and energetic (you should accurately describe your skills instead)
• Saying references are available upon request (you should assume that the prospective employer knows this)

These all sound like great points to me, and I hereby pass them on. However, my point with this post is to ask what use it really is to do so. What use is it really to do so? Why should anyone give away this advice at all?

The reason I ask is that the job-market surely is a zero-sum game. There are at any one time only a finite number of jobs, and presumably those jobs will be filled. At least, those that won't probably aren't filled because applicants didn't have the world's best résumés. Of course, passing this advice on to your friends has a direct benefit to you - that is, if you care more about your friends than about everyone else. But giving away this advice on the internet? Is that because one cares more about job applicants who read stuff on the internet?

It's seems a little like commercials and advertisements: Who do they benefit? Ignoring the fact that commercials are very often misleading and deceitful (and if you don't know which ones tell you lies, then how can you trust any of it?), nearly the best thing one can hope for is that they shift market shares. A new detergent - no different from the nine brands already on the shelves - can conquer a large percentage (though not more than 100) of the market with an enticing ad campaign. But it doesn't make people do more laundry, does it? (Not that that would be a good thing, either.) Rather, it takes away market shares from other companies. And it's not that I care which company survives, or even that we have 9 rather than 10 that do (though I guess I don't prefer monopolies), but I care that so many resources are spent making and watching commercials. It is, like coffee, wasted resources on a planet that is already not able to feed everyone the way its resources are currently managed. If the people who make commercials were made to do something useful (and lands for coffee beans were instead used to grow food), perhaps we could make this place a little bit better.

So why? Who benefits from giving away this information? The answer is, of course, that Forbes and Elizabeth Lowman benefits. It's a known fact in evolutionary theory that what benefits the individual often doesn't benefit the whole population. What is good for me is not always good for society. It needn't be bad for society, as in the case of this advice being given away in Forbes, but it definitely does look nice in Elizabeth Lowman's résumé. And I'll admit that it is good to have an educated and competent citizenry, and it certainly doesn't hurt that people can sell themselves well in their job application - as long as it doesn't skew the hiring results in a way that makes it less likely that companies will hire the best person for the job.

Nevertheless, the résumé building advice is hereby passed on, and I think it's pretty good advice, too. And you may very well then ask me why I blog about this in the first place. What's in it for me? And the answer is that I don't know. I just felt like it, I guess. There are definitely people who I'd like to do well, such as friends currently looking for jobs. I could of course just have sent you an email with a link to the article, but I know you read this...

Good luck hunting for jobs!

The mind is a mysterious place

Limits free us? Do we need constraints to create? "We break out of the box by stepping into shackles." On a related note, in How To Write A Lot, the main message is that to be a prolific writer, you have to allot time to write, like 9-11 am every day, which seems like a constraint as well.


Those annoying songs that get stuck in your head are called "earworms". But how do earworms start?

Male-to-female transexuals have brains that are physically similar to other men's. Mostly. But also, the 24 individuals examined had "a smaller thalamus (the brain's relay centre) and putamen (an area involved in motor control) and increased gray matter in the right insula and inferior frontal cortex (regions involved in representing the body, among other functions)." The researchers speculate that this difference could arise from "a constant rumination about one's own body". So I wonder, can thought processes change not only which brain cells live or die, and which are connected to which, but also the actual amount of gray matter?

Can you live with a scientist?

It's not just a hypothetical question. It is a hypothetical question, but not just. See what I mean? Isn't that annoying? Yes or no? Why do you think it's annoying? Enough with the why-questions, already?

Do couples who are both scientists form couples because they meet in college, or because no one else can stand being around them? Adorable as some people find geeks, my feeling is that some of those some end up frustrated with the geek despite the initial infatuation.

I'll admit it does take a certain patience at times to live with a scientist. They can be annoying in their insistence on understanding things, and in both colleagues and myself I see that the problem is that this insistence can drive other people less interested in comprehension crazy.

Does this all sound too personal yet? Too close to home? Too icky?

You know what? I don't care, because I am happy being the inquisitive person that I am, and if you can't live with that, then you can be on your merry way. It's not exactly that I look down on people who can't handle a scientist (and the truth). Not exactly. But close. Is that arrogance? People have called me that on more than one occasion, so given a scientist's healthy love for statistics, perhaps I should accept that. In fact, let me calculate a p-value for that. Living in four different places, I have found 6, 3, 5, and 8 who called me arrogant, while 4, 1, 0, and 5 said I was not. A one-tailed t-test gives p=0.0423, which means I am statistically arrogant.

Okay, so that was annoying.

What annoys you about scientists? Even if you like them at times, or "all the time", is there ever something about their personality that drives you nuts on occasion? People who have ever broken up with someone - how much was their scienticity a factor? I'd love to hear from other people.

Speciation in the virtual social world: Facebook vs. G+

It may just be me and the people I follow, but isn't Google+ used more for serious stuff that people want others to see, while Facebook is for whatever friends do to each other. That would make sense, I suppose, given that you can't control who follows you on G+. But does it mean that G+ and Facebook are not really competing for the same niche? Even if there are overlapping functions, as there clearly are, are the two so diverged from each other in function that they will continue to coexist side by side in this virtual sympatric habitat of the internet?


In other words, from whence they both came, are they now effectively different species?

Biological species - and by that I do not exclusively mean reproductively isolated species - may compete for many of the same resources, and yet still remain isolated from each other. This can mean that there is no gene flow between them (or rather, not enough to break down the species barrier), better known as no sex despite all the interspecies love. In the case of asexual species, it can mean that one species doesn't outcompete the other because their ecological niches are different enough that negative frequency-dependent selection saves the species that becomes scarce. I believe Facebook and G+ are asexuals, even though code may transfer horizontally between them, just as with unicellular microbes in the world of biological life. Therefore, as long as Facebook is the best at something not insignificant, and G+ is better than anyone else at some function that people really like, then it is unlikely that one will trash the other.

Niche dimensionality have an effect on speciation. Both theoretically and empirically there is mounting evidence that the more ecological niche dimensions (i.e., traits, such as ability to use a certain resource, or the service of video uploading) between diverging species, the higher the chance that the species barrier will persist (Nosil & Sandoval, 2008; Garant et al., 2007; Gerhart & Brooks, 2009). Think of the chance that two species are going to be different from each other in some essential way: the more things they can do - the higher the niche dimensionality - the more likely that they will not completely overlap in function. And the more distinct they are from each other, the higher the probability that they will not drive each other to extinction.

Negative frequency-dependent selection occurs when it is advantageous to be rare. For example, if two species overlap in the use of some resources, but also both use some resource that the other one doesn't, then when one species becomes scarce, the resource it is specialized on becomes abundant (since that species is the main consumer of it). This in turn makes that scarce species have higher fitness, because there is so much resource available to so few, and it again grows in number. On the other hand, if a new species totally covers the function of another species, then it can drive the weaker species to extinction. I wonder if this is what is happening to MySpace (which I have never used, so I am not sure what the trait overlap is between that and Facebook)? Is MySpace all but dead already?

Same question for Twitter and G+. Is there anything you can't do in G+ that Twitter can do? Couldn't G+ just has well fuel revolutions, or is there a special benefit to a 140 character limit? For mobile devices, perhaps? I do actually use Twitter (@CarnyEvolution), but am guilty of only posting - I can't see why I would go there to get updated on anything ever (but then again, I have not been involved in any revolutions lately, nor do I own a mobile device with the capability).

Mutations, changes in code that alters traits, may eventually make either G+ or Facebook better than the other at everything, and then the other should meet its end. Yesterday I was reading about the history of multi-user dungeons (MUDs), which I played for a while in the early nineties. No one plays those anymore, because they have been superseded by massively multiplayer online role-playing games (MMORPGs) like EverQuest, which do all the same things, but adds graphics, which makes them fitter. In biology, there is plenty of empirical evidence that mutations confer higher fitness to a species (more precisely, to a population) in its current environment (i.e., adaptation), both empirically (Barrick et al., 2009) and theoretically (Østman et al., 2011).

Environmental change may eventually change this situation of hostile coexistence, if mutations don't do it first. The hardware may change again, such that some of the services offered on Facebook and G+ become obsolete. Or user preferences may change, for example by many people being really annoyed with Facebook's privacy policy, leading to massive exodus, and bankruptcy.

So, what's your prediction about the future of virtual online social media? Will G+ drive Facebook out of business by being better at everything? Note that Google does many other things that G+, so it is not likely (at all) that G+ will disappear now that it has some traction, because Google gains lots of fitness from al those other traits (search engine, RSS, maps, YouTube, email, etc.). Google really is like the rats or the cockroaches of this world: hellishly adaptable and not so easy to get rid of. Facebook, on the other hand, aka LinkedIn for teenagers, only does one thing, which is dangerous. But as long as it does this thing better than anyone else, perhaps it will be safe?

References:

Nosil P, & Sandoval CP (2008). Ecological niche dimensionality and the evolutionary diversification of stick insects. PloS one, 3 (4) PMID: 18382680

Garant D, Kruuk LE, McCleery RH, & Sheldon BC (2007). The effects of environmental heterogeneity on multivariate selection on reproductive traits in female great tits. Evolution; international journal of organic evolution, 61 (7), 1546-59 PMID: 17598739

Gerhardt HC, & Brooks R (2009). Experimental analysis of multivariate female choice in gray treefrogs (Hyla versicolor): evidence for directional and stabilizing selection. Evolution; international journal of organic evolution, 63 (10), 2504-12 PMID: 19500145

Barrick, J., Yu, D., Yoon, S., Jeong, H., Oh, T., Schneider, D., Lenski, R., & Kim, J. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli Nature, 461 (7268), 1243-1247 DOI: 10.1038/nature08480

Østman, B., Hintze, A., & Adami, C. (2011). Impact of epistasis and pleiotropy on evolutionary adaptation Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2011.0870

Humans are still evolving, especially right now

I had sworn that I would find time during my postdoc to blog as much as during my PhD. But I was wrong. So, for the first time ever on Pleiotropy, here's a repost of a post from February, 2009 - the month of Darwin's bicentennial. The question is one that I find interest many layman, namely whether humans are still evolving. Of course, what they mostly mean is whether we can expect to see significant morphological changes any time soon - wings, tails, x-ray vision. Probably not, but I would argue that if ever, this is the time to do it, because the larger a population is, the bigger the chance that mutations happen, and therefore the more genetic variation. Genetic variation leading to phenotypic changes is the stuff that natural selection acts on, so the fact that most people survive to reproduce actually means that evolution can happen faster. Just wait for the next big environmental change, and then we might see natural selection taking humans in a new direction.

☆ ☆ ☆

Yes, we are still evolving

On RichardDawkins.net I learned that BBC has published a magazine celebrating Darwin's bicentennial. It's in the February issue of Focus, the BBC’s award-winning science and technology magazine.

Dawkins wrote the editorial, Carl Zimmer a piece on Rich Lenski, who studies the evolution of E. coli as it happens, among other things, someone wrote some stuff about artificial selection, and someone wrote about what we have learned since Darwin, and then... Then there's Steve Jones and PZ Myers, two "leading evolutionary biologists," who each give their answer to this question: "Has our species's evolution comes to a halt?" In other words, are humans still evolving? I don't know Steve Jones, Professor of Genetics and the University College London, in any other context (but see this older post on the same subject), but I am a frequent reader of Pharyngula. Neither professor is a leading evolutionary biologist. Jones is a geneticist, and PZ is a developmental biologist. It's a small quip, but since they are discussing evolution, perhaps it is worth taking into account.

Steve Jones says 'yes', and PZ says 'no'. Jones' answer is the controversial one. It is also the stupid one. He clearly does not understand evolution very well. Just trust me. Okay, don't trust me. Here's what he says and why it's wrong.

Jones' claim is that because mortality before the reproductive age has almost vanished, there is no selection going on in humans anymore, and as a result we are not evolving. He gives examples of men in the past who had hundreds of children while other men had none. This is selection: differential reproductive success.

Now, he says, variation in reproduction has all but disappeared. Most people have between zero and four offspring. Thus, he expounds, the variation that selection could favor among is gone, so we are done evolving.

Nonsense.

First of all, zero or four offspring makes a big difference for evolution. In fact, if everyone had one child, except one man who had two (and his children had two each, etc.), then his lineage would soon dominate completely. Zero vs. four makes a huge difference.

Secondly, it is a common misunderstanding that natural selection is a prerequisite for evolution. It is not. All that's needed is heritability and variation. Neutral evolution due to random sampling will take care of the rest (also named genetic drift). Neutral evolution will result in a lot more variation in the (human) population compared to the case with selection. The effect of selection is to reduce variation within a population (but increase it between different populations), so as long as there is no selection, any genotype/phenotype is as good as the other and the population will become more and more diverse.

In humans today there is a great deal of neutral evolution going on, but selection obviously still has a large effect. Just think of genetic diseases. Cystic fibrosis, Tay-Sachs, and Huntington's disease are examples of horrible, heritable diseases, and the unfortunate people who have them are strongly selected against. Additionally, spontaneous abortions happen all the time, and it is likely that many of them are caused by deleterious mutations in the either one of the parents or in the fetus. Additionally, sexual selection may be at work. The more attractive specimens may in fact end up having more children. And then there's the fact that some groups of humans have more children than others (at the moment), such as the Quiverfull, the Congolese, and the Malagasy (source). Selection for reproductive strategy, as in 'the Lord tells me to keep churning them out.'

Another important point to make is that people have different things in mind when they think about evolution. For instance, recalling the notorious micro/macro-evolution dichotomy, in which microevolution is (merely) a change in allele frequencies, whereas macroevolution is speciation and the origination of new traits, such as exoskeletons, blindness, and telepathy. If you mean only the latter, then you might have a point, because right now we don't see these big changes in humans. No one seems to be getting new abilities X-men style or less.

Evolutionary biologists generally agree today that the micro/macro distinction is invalid, in the sense that they are not separated by different mechanisms. A lot of small changes in at the genomic level (micro) accumulates and can eventually result in significant morphological/physiological/anatomical changes and the birth of new species (macro). (Creationist will frequently make this distinction saying that microevolution is possible, but that macroevolution does not follow.) The problem is just that these things naturally take a very long time. 'Millions of years' is an oft quoted span of time necessary for such events (though there is recent evidence in other species that much, much less time is needed). Since humans live and have recorded their own history for a very, very short time compared to a million years, we should not expect to see major changes happen in our lifetimes. The fact that we then don't should not lead us to conclude that we aren't evolving. Have a little patience!

As for selection, it is an unstoppable process. PZ Myers nearly ends his essay in the Darwin 200 magazine thus:

Selection is a subtle force, and you cannot escape it.

Carnival of the fittest

So, despite voicing concerns that the Carnival of Evolution is in a slump, it was posted on time yesterday, and contains 26 posts. Which is in the lower end (hmm, I'm considering generating some stats on this now), but still more than enough for a blog carnival - if you compare to many other carnivals, e.g. on BlogCarnival, you'll see 26 isn't so bad after all.

This is the hand of Australopithecus sediba [wiki], a 2 million year old fossil. What was the use of this hand? It has been suggested that it was used to handle tools, and thus that this was the reason it came to look like this. And by inference, that our hands evolved for tool use. But is there evidence for this explanation, that there was selection for hands that could handle tools? Ken Weiss argues that there is not, and that an equally good explanation is that they evolved for masturbation.

However, as hypotheses, I still think we can differentiate. Ken admits his hypothesis may appear silly, but explains that there really isn't evidence for either one. So okay, I can also come up with a hypothesis that is even sillier (I surmise that hands evolved as adaptations for sign language*), but some hypotheses are more equal than others, I'd say. Tool used may be a "tired old idea", but it's still a viable one.

Also on Carnival of Evolution.

* Wait, that may not be so incredibly silly after all...

Carnival slump?

What's up? Seems to me the number of submissions to Carnival of Evolution is not. This summer we had one edition with 60+ submissions, but last month is was down to less than half that. And it looks like tomorrow's November edition will be the same, because right now I see only 27 posts submitted on BlogCarnival.com, and some of those are spam.



Are people just writing less about evolution these days? Or are bloggers feeling that carnivals matter less than they used to think, so they can't bother submitting? Is creationism winning, with more and more science bloggers avoiding topics in evolution?

I, for one, am blogging less these days, or months, but I have excuses. What about the rest of you? Are you also inundated with teaching, applications, deadlines...? Emotional upheaval? If so, I get it. Otherwise, you can submit right here.

Get some ignorant science advisers now!

It's *almost* hard to tell whether this republican science adviser is for real or not. The giveaway is of course that republicans don't have those...?

We will survive

For Christie, who writes so eloquently about the pain of loss of loved ones.

I lie flattened, like the weight of his words has literally crushed me. I need to do something, anything to lessen this ache. The thought crosses my mind to self medicate, but I quickly decide against that. Mild analgesics like ibuprofen would be useless, as they act peripherally, targeting the pain nerves which send signals to the brain. In this case, it is my brain that is causing the pain. I would have to take something different, like an opioid, which depresses the central nervous system and thus inhibits the brain’s ability to feel. Tempting as that might be, painkillers are an easy – and dangerous – way out. No, I need to deal with this some other way.

Ayala donates $10 million to science

Francisco Ayala is donating $10 million to the School of Biological Sciences at UC Irvine - money earned from his vineyard. The Templeton Prize money he earned last year was donated to UCI as well ($1.5M).



Read the accompanying interview about his work and about accommodating religion and evolution:

Q. Is there a tendency in our society to mix up religion and evolution?

A. I am afraid largely so. I think it is wonderful to teach the Bible, but not to pretend the Bible is an introductory textbook for biology or astronomy.

We succeed in keeping these kinds of things out of the schools, but then the impact on the public at large is not as good as you would expect to have. In the last few weeks, two or three of the Republican presidential candidates have expressed skepticism about evolution. And yet, evolution is confirmed as much as any scientific theory, and better than most. Evolution is confirmed as well as (the idea that) the Earth goes around the sun, or that matter consists of atoms.

It's a matter of scientific ignorance. It's a matter of religious ignorance; as you surely know, most religious authorities, most
churches, are in favor of evolution. As, famously, an Anglican minister -- a theologian -- said, (evolution) appeared first as an enemy, and has turned out to be our best friend, because evolution can now explain all of these sorts of cruelties or mistakes that exist in the world of life.

Let's start with a simple example. The human jaw is not large enough for all the teeth. So we have to pull wisdom teeth -- sometimes one, sometimes two, sometimes three, sometimes all four. An engineer who designed the human jaw would be fired. And yet here we are, saying that would have been designed by God.

Much more extreme and much more serious is the human reproductive system. The human reproductive system is a mess. Twenty percent of pregnancies end in spontaneous abortion, or miscarriages, in the first two months, because the human reproductive system is so badly designed. They blame God for 20 million abortions per year; there are about 100 million births in the world a year. [Emphasis added.]

If evolution was first an enemy and then a best friend, then how does the negation of a literal reading of the parts of the Bible that speak on biology (and other sciences) not call all of it into question?

No one lifts a finger for Chinese girl run over by van

Without questions, this is the most horrific video I've watched in my entire life. You might not want to see it, but everyone should know about it.

A two-year old Chinese girl is in the street alone (!), and a van runs into her, knocking her over, and then drives over her with the front wheel. After stopping for seconds, the van continues, running the girl over with the back wheel.

Lying bleeding in the street, people on foot and in vehicles just pass by her without doing anything. Later, a truck actually runs over her again.

Reports: 1 2 3

What the fuck is wrong with you people? When did a life become so worthless? Shit.

Many people in China are hesitant to help people who appear to be in distress for fear that they will be blamed. High-profile law suits have ended with good Samaritans ordered to pay hefty fines to individuals they sought to help.

---

Update 10/21:

The little girl has now died from her injuries.

Please stop it with the commas!

Lately I have been reading a bunch of papers. I'm teaching a seminar course on evolutionary dynamics, taking a seminar course on multidimensional selection, and I am writing a paper on metagenomics that requires a lot of reading too. So I'm getting picky about commas. It's pretty annoying when people overuse them. I don't care whether there is a consensus that it's appropriate to put them all over the place - even if there is, it's still annoying.

People really like to put them after the first word or first few words in a sentence, as if some big a cumbersome sentence awaits, and for which we must be prepared by taking a deep breath for god measure. For example, one paper had this in the first line of the abstract: "Here we describe, the longest microbial time-series analyzed to date..."¹ The hell? What is that comma doing there? Much more common is to write "Here, we cluster networks..."² But to what end? What is the function of that comma? Are we not really doing it here? Here, we are?

What if I wrote the first paragraph like this:

Lately, I have been reading a bunch of papers. I'm teaching, a seminar course on evolutionary dynamics, taking a seminar course on multidimensional selection, and, I am writing a paper on metagenomics that requires a lot of reading too. So, I'm getting picky about commas. It's pretty annoying, when people overuse them. I don't care, whether there is a consensus that it's appropriate to put them all over the place - even if, there is, it's still annoying.



References:
1. Gilbert et a;, 2011, Defining seasonal marine microbial community dynamics
2. Rahat et al., 2007, Cluster conservation as a novel tool for studying protein–protein interactions evolution