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

Artificial Life 13: Call for papers

Artificial Life 13

The Thirteenth International Conference on

the Synthesis and Simulation of Living Systems

“Evolution in Action”

July 19–22, 2012, Michigan State University

East Lansing, Michigan, USA

www.alife13.org

You are invited to submit papers to the upcoming Thirteenth International Artificial Life Conference.

The 13th conference for Artificial Life is going to be held next year here at Michigan State University. Dates are July 19-22, 2012, and it's going to be a blast, because we'll have great keynote speakers (Benner, Catts, Kerr, Nagpal, Szostak), and lots of sessions on various aspects of evolution (evolutionary dynamics, simulations of evolution, experimental evolution, viral and bacterial evolution, evolution of drug resistance). I went last year and gave a talk on the structure of complex fitness landscapes (pdf), and was happily surprised at the number of evolutionary biologists there. Next year will surely be the same.

Center of the 99% world

The anti-Wall Street protests going on in the states and elsewhere(!) have a website. There you can find your local Occupy Together group - and I suggest you go join them.



What I wanted to point out here, though, is that the map they have on the site with "meetups" has a curious feature. If you start zooming in and keep going, you'll end up right where I live, in East Lansing, Michigan. Try it.

Anyhow, I just thought that was weird.

P.S. Oh, and something about evolution...

Carnival of Evolution #40 at last

The 40th Carnival of Evolution is up today at Kevin Zelnio's blog, EvoEcoLab at Scientific American.

Next month it will be over at EcoDevoEvo aka The Mermaid's Tale. Never too early to submit...

Submit to Frontiers in Genetics

As a first for me, I have been accepted as a member of the editorial board of the new journal Frontiers in Genetics. I'm very excited about this, particularly because I think the particular model of peer-review might benefit science a lot: Articles will be peer-reviewed for correctness, followed by an open online post-review by readers. It's sort of like PLoS ONE in that manuscripts don't have to present completely novel ideas, but with the added post-review by peers that will determine it's impact on the field.

Whether this will work better is an empirical question, and I look forward to seeing the outcome: Will science benefit by shorter time from submission to publication? Will costs be reduced and less money going directly from tax-payers to journals (journals take money from authors to publish, and cost money to subscribe to, and yet ask for a free service from reviewers)? Changing either or both of those would be a step in the right direction.

Specifically I am a review editor for Frontiers in Evolutionary and Population Genetics, which you are hereby encouraged to send your manuscripts to.

My love of kiwi

Clearly, I'd say, love has some evolutionary significance. Why do we love each other? Evolutionary adaptive reasons seem quite convincing: people in love have sex, sex makes babies, and people in love take care of each other, thereby incrasing chances of baby's survival. What a wonderful reward it all is! But what happens in the brain, and why does it feel so bad to lose the one we love? This blog post on Big Think looks at the neurological and chemical underpinnings of this most wonderful human(?) emotion, and what is has to do with sex.

Love is in the brain: That said, it appears that when people are in love, among other neurological activities, two parts of their brain really get activated. They are called the caudate nucleus and the tegmentum. The caudate is a reward center of the brain, and the tegmentum is a region of the brain stem that sends dopamine to it; dopamine tracks how rewarding something is. I get this with food, for example when I eat the perfect kiwi.

And drugs do it too: In effect, being in love rewards the pleasure centers in your brain, which then crave whatever it was that was so rewarding – in other words, your beloved. Those reward centers are the same ones that light up when people win the lottery. Or use cocaine. But love is a double-edged sword, and when it goes wrong it can haunt us like a vendetta.

Indeed, love literally hurts: And being rejected in love activates a part of the brain called the insula, which is the same region that lights up when we are in physical pain. So we are doubly motivated to hold fast to the object of our love: feel the pleasure, and avoid the pain.

Really.

Evolution favors those that feel love, if we believe that the emotion is adaptive. Hard to test, but still a pretty persuasive idea.

Happiness is irrelevant, resistance is futile

When I was a child, I once watched an animated kid's program about a family where the youngest of two children turned out to be retarded. At first the child was just happy, and all was joy. But then later on, the parents got worried that the child didn't respond much, but was just happy crumbling up paper and listening to the sound.

A doctor told them that there was nothing wrong with their child, but that she was just one of "them". At first the parents got really sad and worried, but then the older child said "but look! she's happy!", and then they all realized that this was good, and they that everything was going to be all right.

For me as a child it was a good story to hear (rather than Dragon Ball Z GT total brainless waste of time kind of thing). It made me think. The morale was perhaps that as long as someone is happy, things are really all right. Something like that.

But...

Is that true? Is happiness really the ultimate measure of worth? Does the pursuit of it really make sense to write up as a guiding principle? Is everything okay if we're happy? Can we be happy in other ways than being happy?

I will counter that happiness can be made to stand alongside other measures of a good life. That is, rather than saying that happiness is achieved given we work well, carry out our duty, live up to our responsibilities, treat others well, honor thy parents, score many touchdowns, or whatever you think are good things to do in life, I would say that happiness can be added to that list. Happiness is a thing to achieve for sure, but need not be the ultimate goal. A life can be lived to the fullest without happiness necessarily playing a big part.

For example, people sometimes say that flow is one way to be happy: when we are so immersed in a task that we notice nothing else, then this is one form of happiness. But, while I agree that flow is nice, I do not think it is happiness at all. Rather, it makes happiness irrelevant.

And this is my point here: Happiness is not enough. It is one thing among many that are worth striving for. Rather than being what we may achieve when everything else is right, we can make life worthwhile without being happy (note that not being happy is not equal being unhappy). And also, we can be happy at times without anything else going our way.

In evolution, I could add, happiness is irrelevant. Fitness does not come to the happiest. The happiest human beings are not at all those with the most children. Does the one who have the most children become the most happy? Or does the happiest person become the one with the most children?

Surely a life lived in pure and constant happiness induced by a constant intake of heroin cannot be deemed a good life. Of course a life lived as the happiest retard is not something to aspire to. Clearly happiness is not everything.



Happiness is a warm gun, yes it is.

The beliefs of others... they matter!

Margaret Morgan just alerted me to this old xkcd comic. Old, but unfortunately more pertinent than ever.



So many people have told me that it is a fools errand to care what other people believe. Or that it's just none of my business. Or that I am arrogant to even have an opinion about the beliefs of others.

Well, as this comic illustrates, the beliefs of others sometimes matters in very tangible ways. Besides, religious people impose their beliefs on others all the time, as when they go door to door telling us that we are going to hell*, or when they pass laws based on ancient texts written by homophobic bigots.

* Actually, as I learned the most annoying way, Jehova's Witnesses don't believe there is a hell at all. Boring! Her daughter sure looked like she lived there.

A blog you don't want to be featured on

Retraction Watch. Tracking retractions as a window into the scientific process.

Collecting cases of retracted scientific papers, this blog keeps track of scientific sinners. Whether the retractions result from honest mistakes or from downright fraud, you can find out about them here. Pretty cool. Except for the sinners.

Let it count as a warning for all of us: be careful who you associate with. Should you be an author (particularly a senior author) on a paper primarily written by someone else, make damned sure that the analysis is correct, that the data are genuine, and that the text is original.

The American Family Association still strong on homophobia

It's been quite a while since I last heard from the American Family Association. I was signed up on their mailing list, but then one day those emails stopped coming. I suspect they found out I commented on their stupid endeavors to boycott various companies because they "support the homosexual agenda".

But no worries. All their foolery are available on their website. Among the items is a call for boycotting Home Depot, because they sponsored the San Francisco Gay Pride parade and festival. AFA call for Home Depot to "remain neutral in the culture and political war over homosexual marriage".

There's nothing like religion to excuse homophobia.

Carnival of Evolution #39, and notes on how to help

September 1st edition of Carnival of Evolution has been up for a couple of days already at The End of the Pier Show - biology editor of Nature Henry Gee's blog.

Despite carnivals going extinct here and there, CoE is doing really well. When I can get my act together, it is really no problem finding hosts; right now all slots are taken through January next year (go here and click on 'future hosts'). And while the number of submissions does vary quite a bit - between the low thirties and to over sixty - there are always plenty for the host and readers to dig into. Probably few people get thought them all, except of course for the host who has to, and that is easily a full days work, if not more. So from here a heartfelt thanks to all past and future hosts, and everyone doing what they can to keep CoE running, whether it be by submissions or by linking on their blog, tweeting, updating their FB status, announcing CoE at conference talks*, making it required reading in college, etc. Thanks!

I'm often thinking about new ways to improve the carnival, both in terms of making each edition better and in terms of increasing the number of readers. It's up to the hosts how to put the CoE together, though suggestions are allowed. If you have good ideas that you'd like to share, you'd be welcome to let us know (comments, email, @carnyevolution #carnyevol). And if you think of new ways to promote CoE, feel free to let us know that too. Right now, when a new edition is up, an email is shot out to the email list, which has some 80 contacts, and then a number of people link to CoE on their blog (though that number is usually not greater than ten or so, which I think is too little). If you have done that, go ahead and put a link to your blog in the comments of that edition, like this. And I tweet (ir)regularly now, so perhaps a few of the current 442 followers find their way to it like that. But I really don't know, as I never get around to asking the hosts to find out how many visitors they get to their edition and how they get there. Except, when Larry Moran hosted last month, he showed me that visits went up an order or magnitude compared to the baseline, which was mostly due to a link on Pharyngula. Oh how I wish PZ would link every month, but alas that is like getting the attention of a celebrity.

Now, go check it out.

* Incidentally, I did this recently, and I got nothing but blank stares from an audience of about 200.

On theory and hypothesis

This article in the Washington Post is very tough in creationism, which I can only agree with. For example:

Evolution could not have produced a single mother and father of all future humans, so there was no Adam and no Eve. No Adam and Eve: no fall. No fall: no need for redemption. No need for redemption: no need for a redeemer. No need for a redeemer: no need for the crucifixion or the resurrection, and no need to believe in that redeemer in order to gain eternal life. And not the slightest reason to believe in eternal life in the first place.

It's a great thing to read in such a prominent newspaper.

However, the author, Paula Kirby, also reiterates a characterization of 'theory' and 'hypothesis' that I vehemently disagree with:

In everyday English, 'theory' can mean something vague, a hunch, a guess. In scientific English, it is almost as far from that meaning as it's possible to get: in science, a theory is the best explanation for a set of facts. It carries real weight: in science, nothing can be called a 'theory' until it is very well established indeed. Science has its own term for what, in a non-scientific context, the rest of us might call a 'theory': the scientific term for a suggestion, a best guess, something that seems plausible but has not yet been shown to be reliably true, is 'hypothesis'. You will never, ever hear a scientist talk about 'the hypothesis of evolution', for the simple reason that evolution is long past that stage. Evolution is a theory in the scientific sense of the word - tested, researched, explored and supported by masses and masses of evidence. There may still be specific details that are not entirely agreed upon; but the fact of evolution itself is not disputed by any reputable scientist.

It's a common misunderstanding that those two words convey degrees of certainty in science. They do not. A theory need not be "very well established", and a hypothesis is not necessarily something that has "not yet been shown to be true".

Rather, in science, a theory specifies a cohesive explanation of a natural phenomenon. A theory is a model of how something works, and can produce several hypotheses that can be tested. For example, gravity is a theory of how masses attract each other and other related phenomena (and it is a fact that the phenomenon of gravity exists), and one hypothesis that comes from that theory is that that a hammer dropped above the surface of the moon will fall down to the surface. But again, neither theory nor hypothesis need to be true to be called theory and hypothesis. There are theories that have been shown to be wrong, and yet we still call them theories. The theory of the ether has been shown to be wrong, but it is still a theory. The theory of homeopathy has been shown time and again to be false, and yet we can still refer to it as a theory.

Similarly, a hypothesis need not be a tentative statement of fact. It is a hypothesis that a hammer will fall down to levitate over the moon, but even when that hypothesis has been tested, it is still a hypothesis. It is a disproven hypothesis, but nonetheless still a hypothesis. In everyday English, it does indeed connote uncertainty, but not so in science. For example, we can still refer to both the 'null hypothesis' and our pet hypothesis even when the evidence favors one of them over the other. It's a hypothesis that the hammer will levitate, and while it has been shown to be false, but it can still be termed a hypothesis.

At least, this is how I use the words, and I am a scientist (but see impostor syndrome).

Payback Charlesworth style

Ruse on the left, Charlesworth on the right.

A few days ago I told the story of an exchange between Michael Ruse and some member of the audience at ESEB 2011.

On the train from Tübingen to Stuttgart I sat next to Brian Charlesworth. We spoke about research and the conference, and also about Ruse's talk. I commented how amusing I found the above exchange, and Brian joyfully let on that it was he who had voiced his disagreement. Brian gave the final plenary talk at the conference, and with a smile on his face, he recalled how he in his talk had mentioned that Haldane has written so lucidly about evolution, and that perhaps that was why certain philosophers had trouble appreciating him, since lucidity is not the strength of philosophers in general. Har! Hear hear. Rumor has it that Ruse didn't find that comment all that amusing, but I'm not so sure.

Michael Ruse at ESEB 2011

I'm at ESEB 2011 in Tübingen (website, Twitter), and saw Michael Ruse give a talk today titled What, if anything, does a historian and philosopher has to say to real scientists?

At one point he showed these pictures of Fisher, Wright, and Haldane (left to right), and said that out of those there could be no doubt that it was Fisher and Wright who were the heavyweights. One person in the audience made a sound to disagree, which made Ruse look at the clock and say "in 9 minutes you'll get your chance - if you're a graduate student*. With a comment like that I rather suspect you are."

Major laughs.

As for the answer to his query, I rather fear the answer is "no." At least, he didn't explicitly say anything to the contrary.

* At ESEB 2011, graduate students can raise a page in the program with a green hand to indicate they are graduate students, which will give them priority in the discussion.

Can Michelle Bachmann embarrass herself more than this?

The answer is without a doubt that, yes she can. And I can't wait for the next bigger blooper. While wishing Elvis happy birthday on the day he died is hard for most people to top, I think Michele has got it in her.



How can anybody take her serious as a candidate after dissing Elvis so badly? Surely she could never take Tennessee now!? And the answer to that is that lest we forget, her backers are the craziest of the craziest in this nation of crazies: the Tea Party movement.

Scandinavians have bigger brains for better vision

No matter that this study proposes that people of the north have bigger brains than those at the equator merely to cope with lower levels of sunlight - it would still cause an uproar if the rather large group of people (including scientists) who regularly commit the moralistic fallacy should ever hear about it.

We demonstrate a significant positive relationship between absolute latitude and human orbital volume, an index of eyeball size. Owing to tight scaling between visual system components, this will translate into enlarged visual cortices at higher latitudes.

Bigger brains, and by usual (though not in this case) inference, higher intelligence ranks at least as high on the list of taboos as race does. Telling someone they are less intelligent is one of the worst things one can say about another. As a consequence, research into intelligence is under more scrutiny than most other disciplines, and freely voicing hypotheticals can get researchers fired.

In the world of bats, saying someone has substandard echolocation is not politically correct. Among snails, calling someone fast is frowned upon. Elephants are known to ostracize those claiming to have longer trunks that others. Because if a bat or snail or elephant is substandard in the prime measure of worth, then the fear is that they will be treated badly by those with better echolocation, speed, and trunks.

But luckily (eh?), the study does not suggest any difference in intelligence after all. Just that we Scandinavians have bigger brains because we need to be more sensitive to light, because there is less of it. Phew! Perhaps now we can even use this data to cancel out any differences in intelligence? After all, that there should be any systematic variation in intelligence among human populations is, unlike many other traits, just unthinkable!!!

</sarcasm></exasperation>

Reference:
Pearce, E., & Dunbar, R. (2011). Latitudinal variation in light levels drives human visual system size Biology Letters DOI: 10.1098/rsbl.2011.0570

Evolution meetings in August

Right now the BEACON congress is going on at Michigan State University (Twitter #beacon11). Participants from all five member institutions are here (UT Austin, U Washington, U Idaho, NC A&T, MSU). Program is here (PDF).

While the BEACON congress is a little for the initiated, the European Society for the Evolutionary Biology meeting in Tübingen later this month is not (Twitter #eseb11) . I'm giving a talk there on a paper on epistasis and pleiotropy that I blogged a little about earlier. Anyone else going to Tübingen?

I'll be missing the evolutionary modeling meeting in Groningen just before ESEB, which I'm pretty annoyed about. However, I will go to Denmark after ESEB on vacation, and it just so happens that there is another interesting conference there at that time, so I might drop by there a little: Setting Time Aright*. Gatecrashing is always fun.

* Gotta hate that title.

Is this job posting legal?

Brigham Young University is looking for a professor in plant biology (aka botany). I honestly wonder if this is legal:

Plant Biology - Brigham Young University

The Department of Biology seeks to fill a full time, continuing status position in plant biology. Qualified applicants with a PhD, postdoctoral experience, and expertise in evolutionary or organismal biology (including, but not limited to, modern applications such as molecular ecology, systematics, genomics, evolutionary development, and so forth) are encouraged to apply. The successful candidate is expected to maintain an externally funded research program involving both undergraduate and graduate students. Excellence in teaching is required; teaching responsibilities will include general biology, plant diversity, and a graduate course in the candidate's area of expertise. The department offers competitive start-up packages and reduced teaching loads for new faculty. Interested persons should complete a BYU faculty application form at https://yjobs.byu.edu and attach a current CV and statements of teaching and research interests. Questions can be directed to: Dr. Clint Whipple, Plant Biology Search Committee Chair, 401 WIDB, Department of Biology, BYU, Provo, UT 84602.

The review process will begin September 15th, 2011 for this position and continue until the position is filled. Additional department and college information is available at website: http://biology.byu.edu/home. Brigham Young University, an equal opportunity employer, does not discriminate on the basis of race, color, gender, age, national origin, veteran status, or against qualified individuals with disabilities. All faculty are required to abide by the university's honor code and dress and grooming standards. Preference is given to qualified candidates who are members in good standing of the affiliated church, The Church of Jesus Christ of Latter-day Saints. Successful candidates are expected to support and contribute to the academic and religious missions of the university within the context of the principles and doctrine of the affiliated church.

Are they allowed to not include religion in the list of things they don't discriminate against? Are they allowed to give preferential treatment to Mormons?

Other fun stuff at BYU:

Dress and Grooming Standards

Men
A clean and well-cared-for appearance should be maintained. Clothing is inappropriate when it is sleeveless, revealing, or form fitting. Shorts must be knee-length or longer. Hairstyles should be clean and neat, avoiding extreme styles or colors, and trimmed above the collar, leaving the ear uncovered. Sideburns should not extend below the earlobe or onto the cheek. If worn, moustaches should be neatly trimmed and may not extend beyond or below the corners of the mouth. Men are expected to be clean-shaven; beards are not acceptable. Earrings and other body piercing are not acceptable. Shoes should be worn in all public campus areas.

Women
A clean and well-cared-for appearance should be maintained. Clothing is inappropriate when it is sleeveless, strapless, backless, or revealing; has slits above the knee; or is form fitting. Dresses, skirts, and shorts must be knee-length or longer. Hairstyles should be clean and neat, avoiding extremes in styles or colors. Excessive ear piercing (more than one per ear) and all other body piercing are not acceptable. Shoes should be worn in all public campus areas.

Clones, in other words.

Carnival of Evolution # 38 on Sandwalk

CoE #38 is now live on Sandwalk, and there's plenty of interesting stuff there. In fact there are so many posts that it would be overwhelming if Larry hadn't categorized the posts:

• Classification (10 posts)
• Fossils (3)
• Evolution in Action (9)
• Evolution of Behavior/Evolutionary Psychology (12)
• Evo-Devo (3)
• Evolutionary Theory (6)
• Molecular Evolution/Genetics (7)
• History of Evolutionary Biology (5)
• Evolution vs Religion (3)
• Evolutionary Humor (3)

And so, from the winning category, here is Zen Faulkes of NeuroDojo:

We know what Bruce Wayne picked as a “creature of the night”: a bat.

But why are bats so strongly nocturnal? Why don’t we see bats out flying around in the daytime (besides a few out on remote islands)? After all, most people can quickly think of one line of birds that is largely nocturnal.

If a bird had flown through Bruce Wayne’s window, we might have had a very different character in stately Wayne Manor.

Are we doomed?

#SciDoom New Statesman posed the question "Are we doomed?" to a bunch of prominent scientists, but we are all game.

---

Yes, of course we are. Let me count the ways.

I can think of at least seven "levels" at which we could be doomed, and out of those, three are certain but long term, while the rest are less certain but short term: universe, solar system, planet, life, humans, civilization, economy.

The first three are bound to cease to exist, and this is known with certainty. The universe will keep expanding and cooling until the temperature is the same everywhere (wiki). Fortunately this will take a little while. Sooner than that will be the end of out dear sun (5-10 billion years) and with it the Earth.

But life on Earth might be destroyed long before that. A nice gamma-ray burst or a cool meteor shower could annihilate all life on the planet. And much sooner than that we might see humans going extinct for a plethora of reasons. Civilization may cease to exist for a number of reasons, and our economic system may indeed be doomed, which is what I think many people concerns themselves with than any other of those seven levels.

Wearing my evolutionary biologist hat, I worry that we humans as a species are doomed much sooner that I'd like. As much as I can feel disgust in our many greedy ways, I also love so many of the things we do, and would be really sad if we all were to disappear. And yet, I think that is likely to happen. The evolutionary processes that I would credit with this would be bottlenecking, genetic drift, and natural selection. In that order.

For whatever reason, it is likely that the human population will be decimated some time in the future, perhaps even as soon as within the next hundred years. A cataclysmic event caused by global climate change, perhaps?

If anyone survives at all, I predict it will be in a number of smaller populations separated from each other geographically. These lucky few will thus pass through a genetic bottleneck, which will reduce both the effective population size and the genetic variation within each population. Such a surviving population will eventually bounce back and start growing again, and as it does, the genetic idiosyncrasies of each population will be retained, because the isolation of the surviving populations will make them unable to mate with each other and reduce the variation between the populations. Rather, the genetic variation between the different populations will be amplified, since each population is small. Small populations are more affected by genetic drift - the random sampling of genes (alleles, actually) - and so the population will evolve by drift through the generations. Eventually some populations will grow in size, and intra-population variation in fitness will start to matter again. This is because genetic drift is less effective in large populations, just as throwing ten thousand 7-sided dice will give you an average closer to 4 than using only ten dice will (incidentally, I just did that and got 3.9954 and 2.6000, thus proving my point and that evolution is true, no less). The population thus transitions from being at the mercy of genetic drift to being ruled by natural selection.

Natural selection has the same effect as drift, namely to decrease the variation within a population, while it will increase variation between populations. At least this is true if it holds true that the selection pressure isn't similar among the populations. If the environment is different for the different populations, then natural selection will push the populations to evolve differently. This will then result in a number of small, distinct populations evolving independently, each responding to the various selection pressures that the environment subjects them to. A small group of people in Hokkaido surviving a global cataclysmic event that also wipes out the amenities of civilization, will perhaps be selected for being short and stocky to keep warm, while the few survivors on New Guinea will go through rounds of selection (read: die-offs) due to diseases that they eventually will evolve resistance to. Et cetera.

Assuming that the environmental changes caused by the global cataclysmic event are severe enough that the separated populations won't be able to interact (i.e., have sex) for long enough, the different populations will continue to diverge from each other, and speciation will eventually occur. 6-7, say, million years hence, one of these populations will finally get the hang of it, and civilization will again rear its ugly head. The people of New New Guinea will have created technology and science, and because they are no less curious than their ancestral fools who caused the cataclysmic event in the first place, they will eventually figure out their own origins. Among other things they will find that they are closely related to another humanoid species native to Hokkaido - a species with a very different morphology form their own tall'n'handsome physique. Paleontologists will discover that their last common ancestor were a species of humanoid somewhat shorter than themselves, with smaller heads and no tail, not unlike the Hokkaido species.

With new techniques to decipher ancient DNA found at Antarctica, in addition to historical records unearthed in a bunker in the northern hemisphere, New New Guinean scientists eventually deduce that all living New New Guineans can trace their Y-chromosome back to one male from approximately 6.2833 millions years ago. This man had two offspring, both males, who happened to be separated from each other when the cataclysmic event devastated most of the human population of about 7 billion individuals. One of those was in Hokkaido, and the other was in New Guinea. He was, even without a tail, quite tall’n’handsome himself, and more than just quite proud of both his very successful sons.



This was a story of one way of human doom. Following a world-wide cataclysmic catastrophe, most of us will leave no descendants. A few of us will, and if fate will it, those descendants will split into two species (in this case via allopatric speciation). This may not sound much like doom, but humans in our present form will cease to exist, replaced by other species quite unlike our present selves. A beautiful doom, but doom for us nonetheless.

Did I answer the question "are we doomed?" I'm not sure I understood it in the first place, but this is what came out.