Carnivores have bad taste

Pseudogenes are genes that used to have a function, but no longer do. If a gene contributes to an important function for the organism, offspring with deleterious mutations that ruin the gene will have lower fitness, and as a result won't have as many offspring, if any at all. That mutated gene will likely not go to fixation (become prominent in the population). On the other hand, if the gene used to have a function, but no longer don't, then mutations affecting the gene won't be deleterious. Mutations that turn off its expression (so the protein the gene codes for is no longer produced), and mutations that mess up the amino-acid sequence of the protein (so the protein can't carry out the previous function), won't be detrimental to the individual that has those mutations if the individual no longer needs that function. As a result, those mutations can go to fixation either by genetic drift (i.e., at random), or can even be selected for (e.g., when there is a cost to producing the proteins).

However, examples where pseudogenization is coupled to function is rare. A new study published in PNAS links genes that code for taste receptors to specific dietary changes in carnivorous mammals. Basically, animals that do not eat sweets don't have receptors for sweetness (e.g., cats), and animals that swallows their food whole have no receptors for umami (e.g., sea lions, dolphins).


Mutations causing loss of the sweet-taste receptor gene are in red. The exons (DNA coding for a protein) are intact for dog, which can taste sweet just fine, compared to the exons for various other carnivores which cannot taste sweet, the poor souls.


Examples of what the mutations actually do. Looks like they typically cause frameshifts, which makes the rest of the gene nonsense, and introduces stop codons, which causes transcription to stop prematurely. The first one, with Sea and Fur Seals, shows a mutation that messes up the promoter region of the gene, thereby ruining gene expression.


Phylogenetic tree showing loss (diamonds) of Tas1R2, one of the genes coding for a protein that enables animals to taste sweet.

In this way, several species have lost taste-receptors, and they have done so independently. The Fossa of Madagascar™ have lost the gene for the sweet-taste, but their most close relative examined, the Yellow Mongoose, have not. The red diamonds in the this phylogenetic tree indicates in which the gene for sweet taste has become a pesudogene. The results strongly suggest that loss of the gene has occurred multiple times, rather than once in a common ancestor.

Measuring the strength of selection along these branches, the authors found that the ratio of non-synonymous to synonymous substitutions, d_N/d_S (aka ω) is considerably lower for the species that can still taste sweet, compared to those that can't. An ω lower than one means that mutations that change the amino acid sequence aren't tolerated, while those that don't (the synonymous mutations) are.

So this lower ratio means is that there is strong purifying selection on the gene when the gene is still in use, whereas when ω is higher, selection doesn't care much about the gene. However, the best model fit was one where the branches leading to species with intact taste-receptors had ω=0.13656, while the others had ω=0.41974. That is, while the latter is found to have been under relaxed selection compared to the former, the fact that ω isn't (close to) 1 suggest that it selection isn't wholly indifferent to the state of the protein. The authors themselves are at a loss as to the nature of this mechanism:

Recently, sweet, umami, and bitter taste receptors have been implicated in several extraoral functions (36). Pseudogenization of Tas1r receptor genes in dolphins and sea lions and Tas2r receptor genes in dolphin indicates that these receptors cannot be involved in extraoral (e.g., gut, pancreas) chemosensation (36) in these species. Thus, to the extent that these extraoral taste receptors are functionally significant in rodents and humans, these functions must have been assumed by other mechanisms in the species we have identified here with pseudogenized receptors. What these other mechanisms are remains to be determined, and further assessment of the relationships among taste receptor structure, dietary choice, and the associated metabolic pathways will lead to a better understanding of the evolution of diet and food choice as well as their mechanisms.

One of the species in the order Carnivora is the Banded Linsang, which lives in tropical forests of Thailand, Malaysia, Borneo, and Java. I include a picture of it here just because I have never seen this creature before, and because it is super adorable. It is a close relative of cats, and cannot taste sweet.

Reference:
Jiang P, Josue J, Li X, Glaser D, Li W, Brand JG, Margolskee RF, Reed DR, & Beauchamp GK (2012). Major taste loss in carnivorous mammals. Proceedings of the National Academy of Sciences of the United States of America PMID: 22411809

CoE #45 - the bug edition

Adrian Thysse has done something new. He has slaved through all 45+ submissions to this month's edition of Carnival of Evolution (which, in case you have never hosted, you might not know is a lot of work), and this is the result:



Excellent! I predict that before 2013 we'll see an edition of CoE with sound and even cooler animation, perhaps even uploaded to Youtube and CNN. That really wouldn't be too much to ask.

Nothing is unstable

A previous post from almost three years ago keeps getting comments: Another creationist dentist expert on evolution. That's great, even if it is fueled by creationists like anonymous who left this comments a few days ago:

How can an iris, that can't smell or see, evolve to look and smell like a wasp? The skeptics of God remind me of the biblical verse that reads "they worship the created insread of the creator". God also says He has left evidence of Himself through all creation. Just for a time, I challenge you to put down science books, study not read God's word with an open mind and see if you still cannot see God. By the way, where did all the atoms, energy and all the other elements needed for creation come from. You cannot expect a Big Bang to come from nothingness.

If the question was honest, in that the commenter really wanted an explanation for how a plant can mimic a wasp, then that would be intriguing. There are of course explanations, but this creationist of course isn't interested in any of that. The remarkable thing, though, is the notion that the plant needs to be able to see and/or smell the wasp in order to mimic it. What an utterly ignorant understanding of evolutionary theory!



Another anonymous commenter was kind enough to point to this video of Lawrence Krauss explaining how something can come from nothing. Basically, nothing is unstable. That is, "nothing" is unstable. See for yourself:

Is stasis a general trend across non-skeletal traits?

In today's eSkeptic, which celebrates Darwin's 203rd birthday, Donald Prothero writes about the most cited paper in all of paleontology: Eldredge and Gould's Punctuated equilibria: an alternative to phyletic gradualism (1972).

Prothero explains that the revelation was that species (at least as described by fossils) mostly don't change, but rather are in stasis for most of the time. Gradualism, as proposed by Darwin, doesn't describe the change of species very well.

For the first decade after the paper was published, it was the most controversial and hotly argued idea in all of paleontology. Soon the great debate among paleontologists boiled down to just a few central points, which Gould and Eldredge (1977) nicely summarized on the fifth anniversary of the paper’s release. The first major discovery was that stasis was much more prevalent in the fossil record than had been previously supposed. Many paleontologists came forward and pointed out that the geological literature was one vast monument to stasis, with relatively few cases where anyone had observed gradual evolution. If species didn’t appear suddenly in the fossil record and remain relatively unchanged, then biostratigraphy would never work—and yet almost two centuries of successful biostratigraphic correlations was evidence of just this kind of pattern. As Gould put it, it was the “dirty little secret” hidden in the paleontological closet. Most paleontologists were trained to focus on gradual evolution as the only pattern of interest, and ignored stasis as “not evolutionary change” and therefore uninteresting, to be overlooked or minimized. Once Eldredge and Gould had pointed out that stasis was equally important (“stasis is data” in Gould’s words), paleontologists all over the world saw that stasis was the general pattern, and that gradualism was rare—and that is still the consensus 40 years later.

Stasis, which I have blogged about previously, is not nothing, but a phenomenon to be explained. Why would populations not change gradually, as some had expected? The environment does change ever so often, perhaps even what cold be termed gradually at times. Does stasis in the fossil record have to do with the fact that the information we get from fossils are predominantly about the morphology of vertebrate skeletons? Could it be that gradual changes in response to selection causes gradual changes in traits that don't affect skeletons (such as physiology or behavior)? Could there be general features of genetic architecture, for example, that constrains how skeletal morphology can change?

Alternatively, are is there evidence of stasis on other kinds of traits?


Gould, Shermer, and Prothero in 2001.

Program of the Proceedings of the 44th Carnival of Evolution

We are happy to announce the program for the Proceedings of the 44th Carnival of Evolution to be held at The Atavism:

Session 1. Symposium on the evolution of novelty
Session 2. Evolutionary ecology and life history evolution
Session 3. Philosophy and evolution
Session 4a. Experimental Evolution
Session 4b. Timing and tempo of evolution
Session 5. Outreach and anti-creationism

The poster session will start following the last talk, and will be followed by a banquet.

Notable speakers include

Carl Zimmer, The Loom
Eric M. Johnson, The Primate Diaries
Jeremy B. Yoder, Denim & Tweed
John Wilkins, Evolving Thoughts
S. E. Gould, Scientific American
Zen Faulkes, NeuoroDojo

Registration is free, and we hope you can all attend.

Organizing committee:
David Winter, The Atavism
Bjørn Østman, Pleiotropy, Carnival of Evolution

Behe on Behe, and Behe on evolution

I hadn't seen before that Leo Behe gave an interview last year.

He says as well as anyone what is wrong with the argument from design:

As for the arguments from design, such as irreducible complexity or the so-called fine-tuning of the six cosmological constants, I have many reasons for dismissing them each in particular, but one overarching reason would be the common refutation of William Paley’s classic watchmaker argument—the only reason that complex objects appear to be designed is because we as humans create complex objects, and we then assume that complexity is indisputably indicative of a designer. This is an association we make only as a result of what our “common sense” tells us.

A much too much unappreciated fact.

And Behe Jr. on Behe Sr.:

I would like everyone to realize that he doesn’t have any sort of religious agenda and he’s not trying to denigrate science in any way. Long-held beliefs, especially beliefs developed during childhood, operate on a very deep and basic level of thought—almost subconsciously. These beliefs can exist independently in a perfectly honest and intelligent scientist who is simply doing his part to further theories or ideas that he believes are supported by the scientific data. The best way to progress is through respectful and thoughtful discussion and debate, as it has always been.

I wish this to be true. I've met Michael Behe briefly at a conference, and I would like to believe that his mind is merely clouded by his religious thinking (and I hasten to say, in much the same way that most of us are clouded in our thinking in some ways or other - to me, one of the greatest joys* in life is to discover my own delusions).

That being said, take a look at Michael Behe's take on the newest research out of Lenski's lab: More from Lenski's Lab, Still Spinning Furiously (not a site I spend a lot of time on nor link to much, but making this one exception). He goes:

So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.

Seems to me that what he's doing here is confuse the evolution of the whole system consisting of bacteria and virus (which from the outside does end up with the same dynamics of infection), but ignores the really interesting thing that goes on in the virus in response to the changes in its host (the bacterium). First, what a shame that he can't appreciate the evolutionary processes that took place in these experiments. If this is not a blatant example of inability to break free of dogma, then something else is.

Second, I have always had a problem understanding proponents of Intelligent Design, because they seem to at some level agree that evolution does occur, and yet they have problems with research that shows how new things are made. This is the domain of the "designer", apparently. But then, why not just say that that's what he did? ID proponents still - as far as I am aware - haven't described how evolutionary events such as viruses evolving new ways to attack the bacteria look different from when they happen naturally. In other words, there's no way of distinguishing the two ways (which would be a great step forward for the "debate" if someone would take this question seriously), so why don't the ID proponents just say that this is the way the designer does it in the first place? I mean, instead of this yapping about whether some research is profound or not.

* Along singing, dancing, playing, drinking, thinking, eating, winning, losing, procreating, baking, kissing, camping, biking, skiing, and writing in dew.

Link between political views and physiology

It is becoming more and more clear that political views are in fact not completely decided by rational considerations, as common sense would have us believe. Rather, previous studies have shown a link between emotional (i.e., largely uncontrollable) responses and position on the left/right spectrum: "those on the right are ‘distrustful of differences … fear change, dread disorder, are intolerant of nonconformity, and derogate reason’."*

A new study takes this even further, showing that there are physiological differences between people to the political left and right: "compared with individuals on the political left, individuals on the right direct more of their attention to the aversive despite displaying greater physiological responsiveness to those stimuli."

The researchers measured skin conductivity of people as they were looking at aversive images (spider on a face, maggots in a wound, crowd fighting with a man) and appetitive images (happy child, bowl of fruit, cute rabbit).

In the physiological session, participants were shown a series of 33 still images. Each image was shown once and was preceded by a fixation point that was displayed during an inter-stimulus interval. The order of slides was initially randomized and then presented in the same order to all participants. During the slide show, electrodermal activity (in the form of skin conductance readings) was collected using a pair of Ag|AgCl electrodes and standard psychophysiological equipment. Since eccrine glands release moisture as part of sympathetic nervous system activation, and since the rate of movement of electricity across the surface of the skin is a good indicator of the presence of moisture, electrodermal activity has long been accepted as a fairly direct and pure representation of sympathetic activity, making it a good measure of the psychological concepts of emotion, arousal and attention.

The skin of test subjects on the political right conducted more electricity than those on the left when presented with "aversive" images. That is, conservatives react more strongly to disturbing images.


Triangles: political right. Squares: political left.

As good researchers always should, the authors here moderate their discussion of these findings to not condemn:

Rather than using colourful adjectives, perhaps, the proper approach is simply to state that the aversive in life appears to be more physiologically and cognitively tangible to some people and they tend to gravitate to the political right.

They conclude that we can best understand political inclinations as being partly determined by something other than rational discourse, and propose a way forward:

Rather than believing those with political views opposing ours are lazily uninformed or wilfully obtuse, political tolerance could be enhanced and cultural conflict diminished if it is widely recognized that at least part of our political differences spring from subconscious physiological and cognitive variations that lead people to experience the world in fundamentally different ways and therefore to believe that fundamentally different political policies are appropriate.

Even if we recognize that people on the political right experience the world in a different way than those on the left, and that these differences are strongly influenced by genetic and physiological predispositions - perhaps prompting us to view them as pathological - and thereby fostering greater acceptance, it is in my mind by no means given what "left" and "right" means. The far left and far right have quite different meaning in different societies. In Denmark, for example, being on the far right does not imply that one is against welfare or abortion, while in the USA those go hand in hand. In other words, the Overton window can be moved, and the result will be that people who are on the far right will shift their actual political views, while still associating with the political right. What people identify as may be determined by non-rational factors to a large degree (but most likely not entirely), but where it is even possible to locate yourself is evidently affected by public discourse. We should therefore not view public outreach as futile because people anyway (mostly) can't change their minds, but as imperative to shifting what it means to be liberal and conservative.

* The rest of the quote from the paper goes "while Block & Block [53, p. 395] find that those on the right are ‘easily victimized, easily offended, indecisive, fearful, rigid, inhibited, relatively over-controlled and vulnerable’." Hell yeah!

Reference:

Dodd MD, Balzer A, Jacobs CM, Gruszczynski MW, Smith KB, & Hibbing JR (2012). The political left rolls with the good and the political right confronts the bad: connecting physiology and cognition to preferences. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 367 (1589), 640-9 PMID: 22271780.

SOPA and PIPA

These US House and Senate bills will censor the internet. Sign the petition to vote no on both.

What determines rates of ecological speciation?

Speciation models are the most beautiful thing in evolutionary biology. This is widely known, and those who disagree are the crazies. Other models have their place, and empirical evidence for speciation, and insights from there into how speciation takes place are crucial for progress. But real understanding of this question of questions in evolutionary biology only comes once a model is constructed and validated. It is the ultimate goal of scientific work to condense knowledge in terms we can share and peruse, and this we do in models - which you may call theory, but I tend to regard this distinction with distrust.

Case in point is a model of ecological speciation in a population of sexually reproducing diploids adapting to different resources scattered heterogeneously in the environment: Patterns of Species Ranges, Speciation, and Extinction.

Specific questions asked and answered include: What is the effect is limited vs. wide dispersal, i.e., how is the rate of speciation affected by individuals occupying a small geographical area? How does the distribution of resources (food, a place in the sun, etc.) affect the rate of speciation?

And the answers are: The more widely the individuals roam, and the more mixed resources are in the environment, the lower the rate of speciation is. So when individuals only get their resources from a small geographical area, and when there are few types of resources within that area, the more speciation happens.


Examples of environments with many types of resources within a small area (A) and resources distributed such that individuals will mostly find only one type within the area they roam.

With four different types of resources, the simulations are started with only 20 identical individuals in the corner of an area like the ones above. By reproduction and mutation the population grows and diversifies. Whether resource specialists or generalists emerge depends primarily on the two factors already mentioned: range and resource distribution. Specialists, which are very good at utilizing a single resource, can coexist with other specialists when they use different resources. You eat the bananas, and I'll the the leaves, and then we can get along. However, different generalists, in this model defined as those who use more than one resource, may not get along so well, because they overlap in resource use, and so one will tend to outcompete the other. We thus have that the emergence of specialists equates to higher rates of speciation.

Here are some results:



A and B: highly mixed resource environments. C and D: fragmented resources. A and C: low dispersal range. B and D: large dispersal range.

In A there are three specialists using only one resource (red), five generalists using two resources (blue), and two three-resource generalists (green) coexisting.

In B there is only a single generalist (no speciation).

In C there are four specialists coexisting.

In D there is one specialist and two two-resource generalists.

And Birand et al. did lots of simulation runs to get a good handle on the importance of the different parameters governing speciation rates. In addition to the two already mentioned (dispersal and resource distribution), another important one is the strength of trade-offs. It can be set as more or less difficult for individuals to be good at utilizing more than one resource. As an example of trade-offs, think of lemurs: Some lemurs eat leaves, and in order to digest the hard-to-digest cellulose, they have really long intestines. Other lemurs eat fruit containing lots of sugar, which is easy to digest. They don't need to have long intestines for that, so they have short ones, and thus can't digest leaves very well. At the same time, lemurs with long intestines can't eat fruits, because they tend to rot while making it all the way to rectum, which makes the lemurs sick. Thus, there is a trade-off between which foods the lemurs can eat, which makes the two species able to coexist (at least in theory - I don't know if they have overlapping ranges). Competitive exclusion (wiki) prevents lemurs that use the same resources from coexisting in the same area, while two species that occupy different niches won't have a problem with each other.

But, while trade-off are important to have for speciation to occur, varying the strength of it had little effect compared to the effects of limited dispersal and resource distribution.

In fact, geography turns out to be the most important feature in this model:

Indeed, when resources were distributed randomly, which resulted in highly fragmented landscapes (figs. S1, S11), there was always only one species regardless of the dispersal range D and trade-off coefficient b (of the 90 simulations initiated with all the parameter combinations of b and D, only one simulation resulted in two species).

That is to say, if it wasn't because resources are distributed in a patchy way, then speciation just doesn't occur at all. When individuals can find all four types of resources within their dispersal range, then generalists are always of higher fitness, and specialization is not favored. This also means that this model cannot account for (strict) sympatric speciation, where there is no geographical structure, and where individuals are not limited to mate with those close by, or use resources in their neighborhood. Not surprisingly, parapatric and allopatric speciation (where geography is a factor) is much easier than sympatric speciation (where geography is not). For that something else is needed. Stay tuned.

Reference:
Birand A, Vose A, & Gavrilets S (2012). Patterns of species ranges, speciation, and extinction. The American Naturalist, 179 (1), 1-21 PMID: 22173457

My time with Hitchens

So Christopher Hitchens died. It is sad when someone dies, mostly, and it is a good time to remember the good thing about the deceased. When the dead is a person like Hitchens, troublemaker extraordinaire, people will do the usual an extoll his accomplishments, but will also point out the extent to which they disagree with him. I don't personally have a problem with either (and feel quite certain that Hitchens wouldn't either, for what that's worth), and he has been given a lot of praise and taken a lot of flak since his death. But I see it as I do with other great contributors to thought - scientists in particular - that we can take from them what we appreciate and leave the rest for historians. Newton was not a nice person, and likely died a virgin (pft!), but we admire him as the greatest thinker of all time because of his accomplishments. And as for Hitchens, what does it matter to me that he was a drunk and supported the Iraq War? None. What matters is the things he said that I can use.

In spring 2008 I took a course with Michael Shermer at Claremont Graduate University called Evolution and Society. Shermer assigned us to answer the same question that he asked a bunch of luminaries via the Templeton Foundation: Does science make belief in God obsolete? Hitchens' answer is in the newest edition of eSkeptic, titled "No, but it should." That sums it up pretty well, and the substance of his reason why religion ought to be obsolete is captured by his sentence "It [religion] is how we came up with answers before we had any evidence," and thus captures the essence of what is exactly wrong with religion and faith: a lack of evidence and dismissal of evidence.

My own essay is listed here (comments by Shermer in Brackets):

Does Science Make Belief in God Obsolete?

As an atheist scientist, I dismiss the supernatural, and am therefore tempted to rule belief in God obsolete. There are many obvious reasons why – from a scientific point of view - science and religion cannot both be true. To cite just one example, Genesis 1 - what we have learned through science directly contradicts this biblical story of creation. They cannot both be the correct model of our origins.

By itself, however, this fact doesn’t render belief in God obsolete Because belief in God serves multiple purposes. Although science is superior at predicting and describing the world around us, has brought us true insight and utility, and has been used for a broad range of purposes, both good and bad, it cannot do some things that religion does very well.

Judaism, Christianity, and Islam are nearly identical in the way they are utilized by some of their followers, most notably in ways that science cannot replace. This God of a bronze age desert people continues to serve many people very well today.

What this God does for people is to tell them how to behave by word and by example. This frees people from thinking about such moral matters, and justifies the behavior of those who live and act as commanded by God. Many people still believe that it is through God we have our morals, and they cannot imagine a world without a deity to guide them. Logically, there exists no way of inferring how we should behave from what we can learn through science (the so-called “is-ought” problem, or the naturalistic fallacy), and religion thus trumps science in this matter. Science can explain what we come from, but it cannot tell us how to behave.

Belief in God allows some people to make a living without producing anything of value to society. Interpreting scripture and telling people how to live as God commands, they are generously supported by the rest of society [in what way?]. They [who is “they”?] do not contribute anything tangible, but purport instead to be a link to God, and to know what God wants from us [do you mean priests and pastors? In America they are voluntarily supported by their customers, the members of the church, who by making donations signal that they do, in fact, believe there is something of value being presented]. While science requires scientists devoted to the pursuit of knowledge, scientists cost society far less than what it earns from the resulting discoveries.

Throughout history, belief in God has given rulers the justification for their positions of superiority [I think you mean here the divine right of kings concept]. Oppression and tyranny has been, and continues to be, done in the name of God. Kings and emperors would never have been able to control the masses without the belief that God had personally chosen them. World leaders today continue to justify their means by invoking God, and they are often supremely confident that they have the moral high ground over those people who do not share their particular belief, let alone over those who do not believe at all. Science does not do this. It cannot, because it deals only in knowledge, and thus doesn’t speak of superiority. [what about Marxism, and Marxism-Leninism, supposedly grounded in solid social science and applied throughout the Soviet Union and Mao’s China?]

But perhaps more than anything else, belief in God comforts. People are scared of life, and they are scared of death. It’s a frightening world, and we are but dust blowing in the wind, with minimal control over our own fate. Death is final, and that’s all there is [too colloquial, best suited for a bumper sticker] [these short toss-off lines are not sentences]. Belief in God means, perhaps more than anything else, that once you die, you get to go to a better place, where you will stay forever together with your loved ones. Your life on Earth is merely a test, and if you pass it, you will fear no more, forever. Those lewd unbelievers can go to Hell, where they will burn and suffer forever for their unbelief, by will of God, loving and omnipotent. All science does in this respect is tell you that this life is all you’ve got. That’s it.

So belief in God is by no means made obsolete by science. While my professed disbelief strongly suggest a heap of sarcasm [I’ll say!], I honestly mean it when I say that belief in God is extremely useful, just not in any way in which I would like to participate.

I believe that this world would be better place without belief in God. Science has been a way for me to gain comprehension, and thus a way to accept who we really are, and what life has in stall for us. I am also afraid, but I have come to accept that fear as part of who we are. I refuse to join those who extort and oppress others in the name of God. I am a scientist, and I shall not waiver. Faith is obsolete for me – there is nothing that I dare not question.

I met Hitchens when he came to Pitzer College in 2008 to give a talk before a student audience. He hadn't prepared a presentation particularly for this event, but asked a small group of us over dinner what we would prefer, and it was generally agreed that he should talk about atheism. However, at one point he noted that he also had a great memory for limericks, and asked if we wanted to hear some. Second question: Can we handle some dirty ones? General excitement, except from one woman behind me who gloomily went "No. No. No." Among the many he shared, I only recall this one:

There once was a hooker from Q
who filled her pussy with glue.
She said with a grin,
if they'll pay to get in
they can damn well pay to get out too.

And for that, we thank you.

Pun five

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!