Do we really need a new revamped theory of evolution?

A short answer to this meaty question is – NO?

But if you have been keeping a track of science news in the press recently, the half-baked articles all have this vague notion that an urgent extension is needed to the theory of evolution. And if you now ask why do we need such an extension, the answer invariably comes back as – EPIGENETICS.

In this summer we had a major controversy regarding the inadequate and completely wrong interpretation of epigenetics and gene regulation Siddarth Mukherjee’s article in The New Yorker based on his new book – The Gene: An Intimate History (Scribner, 2016). Apart from that, Royal Society conference hosted a conference on “New Trends in Evolutionary Biology: Biological, Philosophical, and Social Science Perspectives.” which harped on bringing a thorough revamp in evolutionary biology. And this was succeeded by a few articles like journalist Robby Berman’s Big Think,”How about a new theory of evolution with less natural selection?” and one by the eminent Carl Zimmer in Quanta Magazine as a longish essay, “Scientists seek to update evolution.”

So, what is this controversy about, who are the  “Third Way of Evolution” group and why despite all these claims evolutionary theory doesn’t require any sort of revision. This post discusses these issues and hopes that it would convince the readers that “All is well” with evolution.

The journos, and the “Third Way of Evolution” group  claim that the rising field of epigenetics is a way by which environment leads to long-lasting changes in the phenotype which can be inherited without altering the DNA sequences directly.epigenetic_mechanisms

These changes come somehow by the presence of methyl groups on a few nucleotides aka DNA methylation. Such changes can then be inherited by the next few generations, and so these folks claim such changes can be subjected to natural selection which leads to a form of evolutionary change similar to the old, bygone Lamarckian theory of inheritance of acquired characters. Apparently, traditional evolutionary theory doesn’t account for this mechanism and hence is in dire need for change!!

But some important aspects which people misread are the following:

  • This form of  neo-Lamarckian inheritance is not permanent and is wiped clean after a few generations. The most touted example of epigenetic changes inheritance in a plant lasted for 31 generations before being erased. And till now, no evidence has come up regarding epigenetic changes being inherited in a vertebrate.
  • When geneticists trace any adaptive changes being found on the genome, what is seen are the actual, real changes in the DNA sequence itself and not on the presence/absence of methyl markers on those nucleotides making up the sequence.
  • The increase in the frequency of DNA sequences which are susceptible to environmentally-induced methylation because them being adaptive is straight-forward natural selection and doesn’t require a revision of evolution.
  • Some methylation changes are indeed coded by the DNA, as in mediating parent-offspring conflict. But this form of evolution is not because of the environment but has happened due to normal natural selection.

Berman in his potpourri article used niche construction as an example of how epigenetics can work . But what he didn’t understand was that niche construction result more from DNA sequence changes which are adaptive to the novel environment the organism encounters and not due to the environment. As Jeffrey Coyne put it brilliantly – “Berman has no idea what he’s talking about here.”

In regards to the much-advertised meeting held by Royal Society – “New Trends in Evolutionary Biology: Biological, Philosophical, and Social Science Perspectives.” many of the attendees were sponsored by the Templeton Foundation which in recent years has led the highly stupid movement of bridging science and religion. It’s been the case that they have funded any project which is woozy and unscientific but sounds sciency/lofty in its aims. Check some of these woozy grants out –

So, this brings a huge doubt as to the impartial scientific motive behind this conference. Are these so-called revisionists simply “careerists” as Jeffrey Coyne puts it? Sadly, in this era of waning grants and increasing pressure to publish in high-impact journals (which itself is a crap idea to measure science) some people have come up with these half sciency, half baloney ideas which promise the moon all the while being blind.

This misunderstanding of epigenetics and the extent of its role is not restricted to these but even respected scientist/Pulitzer-winning author Siddhartha Mukherjee did a similar faux pas this summer with his article in The New Yorker. Nature even wrote an article collating the various viewpoints on the issue. His mistake was not claiming that evolution needs an overhaul but more nuanced, as he said that epigenetic markers play a huge role in gene regulation. What is now known to every biologist is that it’s transcription factors (proteins) which control the rate of transcription from DNA to messenger RNA, by binding to a specific DNA sequence. In turn, this helps to regulate the expression of genes near that sequence. Now, this coming from The New yorker and Mukherjee would convince layman about the role of epigenetic markers in gene regulation despite them not being true !! And the final nail in the coffin was when towards the end of the article he speculated that such inheritance of acquired characters via epigenetic markers (Lamarckism at its best !) could play a major role in evolution. As it’s been said, again and again there is simply no evidence for this and hence needless speculation based on shaky ground is harmful to science.

For more:

  1. The Role of Methylation in Gene Expression
  2. Researcher under fire for New Yorker epigenetics article
  3. The Imprinter of All Maladies
  4. Once again: misguided calls for a thorough revamping of evolutionary biology
  5. The New Yorker screws up big time with science: researchers criticize the Mukherjee piece on epigenetics

Population Genetics Undergrad Class

A nice bunch of notes for learning a wee bit of population genetics. Covers recent advances in pop gen too !

gcbias

We’re teaching Population and Quantitative Genetics (undergrad EVE102) this quarter. We’re posting our materials here, in case they are of interest.

A pdf of the popgen notes is here

The slide pdfs are linked to below

Lecture One [Introduction and HWE]. Reading  notes up to end of Section 1.2.

Week 1

lecture_2_rellys_inbreeding  [HWE, Relatedness (IBD), Inbreeding loops] Read Sections 1.3-1.5

lecture_3_population structure [Inbreeding, FST and population structure]

1/2 class Reading Discussion Simons Genome Diversity Project and Kreitman 1983 + 1/2 class on  lecture_4 [Other common approaches to population structure, Section 1.7 of Notes optional reading]

Week 2

lecture_5_ld_drift [Linkage Disequilibrium + Discussion of Neutral Polymorphism] Reading Section 1.8 of notes.

lecture_6_drift_loss_of_heterozygosity[Genetic Drift & mutation, effective population size. Read Chapter 2, up to end of Section 2.3]

Lecture 7. Finishing up lecture 6 & Discussion of Canid paper.

Week 3.

lecture_8_coalescent. [Pairwise Coalescent & n sample Coalescent…

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Are humans still evolving? Yes, both globally and locally.

An eternal question by almost everyone – Are humans evolving or are we at an evolutionary equilibria (if that even exists). Jerry says we are evolving still. An interesting read indeed !!!

Why Evolution Is True

The one question I’m inevitably asked after lecturing on evolution to a general audience is this: “Are humans still evolving?” What they really want to know, of course, is whether we’re getting smarter, taller, handsomer, and so on. Well, with respect to those traits I always say, “I have no idea,” but humans are still evolving, albeit in ways that don’t excite most people. I’ve posted about this twice (see here and here), and in recent times we have evidence for H. sapiens evolving to produce, in women, earlier age of first birth, later age of last birth and (also in women) increases in height in some places and decreases in others. Studies in the U.S., which haven’t been conducted elsewhere, show the recent evolution of reduced cholesterol levels and lower blood pressure, and an increased age of menopause.

The U.S-specific data brings up the question of whether even if the entire…

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7 MISUSED SCIENCE WORDS

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Now there are various words tossed around everyday with little attention towards their exact meaning. And sometimes, i am simply amused by people declaring themselves Google and charging ahead by using words like ”Theory” or ”Model”.  A recent article in Scientific American titled – “Just a Theory”: 7 Misused Science Words  is just the cure i was looking for.  It starts off by listing those very words which i hate to be tossed up with during a dinner party or worse at a scientific conference !! I will list them out in full below and you can all have fun in reading the actual article in Scientific American.

1). Hypothesis

2). Just a theory?

3). Model

4). Skeptic

5). Nature vs. nurture

6). Significant

7). Natural

Now the above words are something which we all encounter during our school and college education. But the misuse of these words shows that people are not taught how science actually works !! Its not how it is showed in cartoons or zombie dystopian movies.

In the end, i would like to quote from the article itself:

Most people tend to use mental shortcuts to make sense of the cacophony of information they’re presented with every day.One of those tendencies is to make a binary distinction between something that is true in an absolute sense and something that’s false or a lie. “With science, it’s more of a continuum. We’re continually building our understanding.”

Additional readings:

1). What is Science? The Scientific Method, LiveScience Website, 2012.

2). The trouble with “science” (guardian.co.uk)

WELL, FINALLY I BID ADIEU TO THE SASQUATCH/AMERICAN BIGFOOT…

Photo of an unidentified animal the Bigfoot Re...

Photo of an unidentified animal the Bigfoot Research Organization claims is a “juvenile Sasquatch” “Jacobs Photos” . . Retrieved 2009-09-16 . (Photo credit: Wikipedia)

Well, urban legend has it that Sasquatch aka American BigFoot, the name given to an ape-like creature apparently inhabits forests, mainly in the Pacific Northwest region of North America and it has been some decades that people have been arguing about its reality. Last year in September 2012, Dr. Melba S. Ketchum announced with some big fanfare that she and her team from DNA Diagnostics Inc. havesequenced the genome (mitochondrial and nuclear) of sasquatchfrom all the alleged samples people have collected from some time. However, instead just verifying that Sasquatch is nothing but an urban legend they issued this press release:

“Our study has sequenced 20 whole mitochondrial genomes and utilized next generation sequencing to obtain 3 whole nuclear genomes from purported Sasquatch samples. The genome sequencing shows that Sasquatch mtDNA is identical to modern Homo sapiens, but Sasquatch nuDNA is a novel, unknown hominin related to Homo sapiens and other primate species. Our data indicate that the North American Sasquatch is a hybrid species, the result of males of an unknown hominin species crossing with female Homo sapiens.

Hominins are members of the taxonomic grouping Hominini, which includes all members of the genus Homo. Genetic testing has already ruled out Homo neanderthalis and the Denisova hominin as contributors to Sasquatch mtDNA or nuDNA. “The male progenitor that contributed the unknown sequence to this hybrid is unique as its DNA is more distantly removed from humans than other recently discovered hominins like the Denisovan individual,” explains Ketchum.

“Sasquatch nuclear DNA is incredibly novel and not at all what we had expected. While it has human nuclear DNA within its genome, there are also distinctly non-human, non-archaic hominin, and non-ape sequences. We describe it as a mosaic of human and novel non-human sequence. Further study is needed and is ongoing to better characterize and understand Sasquatch nuclear DNA.”

So, one would immediately say -Yay science proved it exists, right? The answer however will be a big emphatic NO. The prime reason is that science doen’t work on hearsay but on repeatable, well-designed experiments with no ambiguity in either the way its conducted or how samples are gathered. And this is where this so called genetic evidence fails big time.

One of the biggest red flags to this whole study is: How did she get her samples? After all, if she was working from a well-reliable source, that alone might be a big sensation because no physical evidence of Bigfoot exists on record. As it turns out, Dr. Ketchum says her DNA sample was obtained from a blueberry bagel left in the backyard of a Michigan home that, according to the owner, sees regular visits from Sasquatch creatures.

And if the sample gathering itself is in doubt, then how can anyone believe the results ? Another face-palm statement: Fully human mitochondrial DNA, which is inherited from your mother, so she assumes that all Sasquatches had human women as relatively recent ancestors, but at the same time, the nuclear DNA is some bizarre menagerie that includes non-ape sequences? And frankly speaking, any biology student would tell you its hogwash !!

But all of this was from last year, and ever since then she has been trying to publish it in a scientific journal and recent news suggests that she has been unable to clear the peer-review stage. So, in response to this, she has decided to start over – recollect samples, do the whole sequencing again, and re-interpret the results…..Naaaaaaa, thats what any other scientist would have done. What she has done is to buy a journal !!  The Journal of Cosmology was available  she bought it and renamed it to De Novo.  One glance at the website and you are reminded of your art school classes in grade 8. The icons are mis-matched, the colour is horrid and the overall design is completely unprofessional. PZ Myers in is blog Pharyngula has it better:

Then she came out with a special edition. It’s Volume 1, Issue 1. It contains precisely one paper, hers.

You should be laughing by this point.

The online journal is a mess. The layout is funky-ugly, it’s difficult to figure out how to actually get to the paper, and when you navigate to it, it’s got a wretched little “Buy Now” button imbedded in a couple of intersecting blocks of color in a hideous table-like layout. It reminds be of the esthetics of JoC.

Anyway, it’s $30 to buy a paper so bad they had to build a custom journal around it to get it published. Not interested.

So, seeing all this mess i wish to bid adieu to Sasquatch !! May it continue to relive in our science fiction movies…

More on this:

  1. Sasquatch is ill-served, Pharygula, 2013.
  2. What I really want to see is the DNA sequence of an alien Grey, Pharyngula, 2012.
  3. Bigfoot in popular culture, Wikipedia.
  4. Is this Bigfoot … or is it a bear with bad skin?, Daily Mail, 2007.

DARWIN DAY !!

It's Darwin Day!

It’s Darwin Day! (Photo credit: Kaptain Kobold)

Darwin Day commerates the birth anniversary of Charles Darwin who was born on February 12, 1809. And on this day, various scientific institutions, agencies and bodies organise lectures and talks to highlight the awesome contributions of Darwin to science. Without his impressive array of work, science would have been quite bare and we quite ignorant about the inner workings of nature.  So, celebrate this day not in the name of Darwin but what science has done for the betterment of humanity in general. Think about all the inventions and discoveries science has brought us and let’s drink to it !!

So, what better way to celebrate this day  than to showcase the Bird-of-Paradise Project of Cornell Ornithology Lab.  The site gives a wonderful description of their project:

The birds-of-paradise are among the most beautiful creatures on earth—and an extraordinary example of evolutionary adaptation. On this site you can find what few have witnessed in the wild: the displays of color, sound, and motion that make these birds so remarkable. Then you can delve deeper, examining the principles that guided their evolution and the epic adventure it took to bring you all 39 species.

GENOMIC EVIDENCE FOR ADAPTATION TO GLOBAL WARMING??

Global Warming – The ultimate quibble of this century !! Or should i say the “haute” of this century. Why? Now, common ask yourselves, which single topic apart from the religion/atheism debate, you always hear in any gathering or book reading circles or conferences or on social platforms which is ready to divide people into two opposing camps. Books are being written, movies made, debates fought and what for – “The legitimacy of Global warming”. Despite numerous evidences detractors still love to question it. However, a new paper published this month in PNAS provides genomic evidence forphenotypic responses to climatic warming.

What’s it all about?

Ongoing changes in regional climates, especially the trend of warming winters and blazing summers are pushing many species (both plants and animals) to shift their distribution toward higher latitudes and altitudes. Such a change in the species distribution, with an expansion in previously hostile areas and contraction in their own habitats which are becoming less favorable, can occur rapidly both in plants and animals. However, not all species can migrate to lesser hostile areas, and there are many reasons proposed for it. Primarily among them is the increasing trend of Habitat Fragmentation. Habitat fragmentation can result from human expansion into wilder areas resulting in few phenomena:

  • Reduction in the total area of the habitat
  • Isolation of one habitat fragment from other areas of habitat
  • Breaking up of one patch of habitat into several smaller patches
  • Decrease in the average size of each patch of habitat

As, a result of such human activity many species especially plants can’t migrate into other areas resulting into their dwindling numbers. But some species do survive in such increasingly fragmented habitats and hence have adapted to the climatic warming. Though some previous studies inDrosophila melanogaster have shown adaptive trait variation in relation to climate change in both natural and experimental population, however in some cases, the evolutionary response to climate change may be slow due to genetic constraints causing a time lag between the environmental change and an observed evolutionary response. Hence,understanding how various species track climate warming bygenetically based adaptive trait variation and which traits facilitate the evolution of such adaption is important.

What is the new evidence?

Thymus vulgaris

The authors decided to look at Mediterranean wild thyme (Thymus vulgaris), a low growing herbaceous plant which is native to Southern Europe and is often used as a culinary herb. The plant contains many oils and the chemical composition(phenolic or non-phenolic) of it varies in different regions based on the temperature. These oils make a plant adaptable to freezing and hence different climatic areas have plants with varying composition of oils (chemotypes). So it would be worthwhile to see if the recent trend of gradual warming of extreme winter freezing events, has brought about an evolutionary response in plants i.e, has their chemical composition changed over time? Interestingly, any such change in the respective oil compositions in different climactic areas with different temperatures would have a genetic basis. And this is what the authors looked about.

The study area had a Mediterranean climate with summer drought but also severe winter freezing temperatures within the basin as a result of a dramatic temperature inversion In this area, there are six differentchemotypes that are the expression of a genetically controlled polymorphism in T. vulgaris. Two phenolic chemotypes (carvacrol and thymol) are largely dominant on the slopes above 250-m elevation and four nonphenolic chemotypes (linalool, thuyanol-4, α-terpineol, and geraniol) below 200m elevation, where they experience the winter temperature inversion. Hence, phenolic chemotypes are predominantly winter non-tolerant whereas non-phenolic types are winter tolerant.

There is thus a sharp gradient in the chemotype frequency over only 3–5 km that goes from 100%of either phenolic or nonphenolic chemotypes to 100% of the other form, with a narrow transitional zone. In short, nonphenolic chemotypes show adaptation to habitats, which in the past have experienced extreme freezing temperatures in early winter, whereas phenolic chemotypes are sensitive to intense early-winter freezing and occur in habitats where extreme summer drought can exclude nonphenolic chemotypes.

Hypothesis: Phenolic chemotypes (thymol and carvacrol) now occur in sites where they were previously absent or have increased their frequency in the transitional sites due to a relaxation of selection pressure normally associated with extreme early winter freezing temperatures due to climatic warming.

To do so, they compared the chemotype composition of populations observed in the early 1970s  to that in 2009–2010 for 36 populations sampled along six transects. Each transect was <10 km long, each containing six populations, with two “phenolic,” “mixed,” and “nonphenolic” populations.

They found that the mean percentage of phenolic chemotypes in a population was significantly (df = 35, S = 68.5, P < 0.01) higher in the contemporary samples (overall value of 53.1%) than in those of the initial study (47.7%) of 1970’s. The changes in composition of the initial nonphenolic populations were associated with the appearance of the thymol chemotype in all eight of the populations whose composition changed and the carvacrol chemotype in three of them.

The changes reported involved a reduced intensity of freezing events and changes in frequency of freezing tolerant and nontolerant phenotypes in natural populations of the Mediterranean aromatic plant, Thymus vulgaris. A significant appearance of freezing-sensitive phenolic chemotypes in sites where they were historically absent and an increase in their frequency in previously mixed populations was observed. Such changes have occurred in 17 of the 24 populations where they could potentially occur.

Such studies, illustrate that a rapid evolutionary response to temperature modifications can occur where genetic variation is combined with a change in a previously strong selection pressure, even for a perennial woody plant. Hence, this provides quite a neat example of genetic changes brought about by climatic warming.  I guess, the detractors of global warming would be feeling quite uneasy now !!

More on this:

  1. Genetic consequences of climate change for northern plants, Alson, Proceedings of Royal Society B, 2012.
  2. Climate extremes: Observations, modeling, and impacts, Easterling DR, Science, 2000.
  3. Ecological and evolutionary responses to recent climate change, Parmesan C, Annu Rev Ecol Syst Evol, 2006.
  4. Ecological responses to recent climate change, Walther GR, Nature, 2002.
  5. Rapid shifts in plant distribution with recent climate change, Kelly AE, Goulden ML, Proceedings of National Academy of Sciences, 2008.
  6. The distributions of a wide range of taxonomic groups are expanding polewards, Hickling R,Global Change Biology, 2006.
  7. A globally coherent fingerprint of climate change impacts across natural systems, Parmesan C, Nature, 2003.
  8. Running to stand still: Adaptation and the response of plants to rapid climate change, Jump AS, Ecology Letters, 2005.
  9. Genetic response to rapid climate change: It’s seasonal timing that matters, Bradshaw WE, Molecular Ecology, 2008.
  10. Climate change and evolutionary adaptation, Hoffmann AA, Nature, 2011.

TO QUIVER OR TO SHIVER !!

The title of this post – To Quiver, or to Shiver is taken from a new article published this month in Proceedings of Royal Society London B. The paper deals with an interesting question – If a organism is good at one thing, does it mean that its good at all others too? OR Do you have to pay a price for being the best at something?

What is it all about?

Parasemia plantaginis coll. Mus. Zool. Oulu

Parasemia plantaginis coll. Mus. Zool. Oulu (Photo credit: Wikipedia)

Wood Tiger Moths, a species of moth(Parasemia plantaginis) found throughout Europe are widely known for their different wing colourations depending on the place they live.

Now why would this moth have bright colours?

Wouldn’t it attract more predators and hence get eaten up?

It turns out colours are used by various organisms as a predator-defence strategy. There can be two kinds of colouration schemes:

  • Camouflage:It  is one colouration-based predator defence strategy and benefits from variable coloration, which prevents predators from developing a search image for the most abundant phenotype of prey.Because, if the prey have a consistent camouflage colouration then the predator would after a few trials and errors, learn to identify the prey easily and then the prey would be wiped out due to the predation pressure.
  • Aposematism: Situated at the opposite end of the predator aversion strategy spectrum, where prey use conspicuous warning signals to advertise their secondary defences. Warning signals of such organisms are not expected to vary much because predators should learn to avoid a uniform signal more efficiently than a variable signal, leading to greater survival.

Now, Wood Tiger Moth the species in question as seen in the picture above show aposematism and use these conspicuous colours as a warning signal towards predators. But, contrary to the predictions for this warning signal homogeneity,  many such moths possess variable warning signals.

So, if uniform colouration is so important for predator defence, then why does the Wood Tiger Moth show variation in colours?

One reason could be that though different hindwing colours (white or yellow) ,in case of Wood Tiger Moth form the basis of predator defence but as one goes towards the Northern Latitudes, melanization or a general blackening of the hindwing is necessary for maximal absorption of sunlight or thermoregulation.

The general blackening to which i refer is the deposition of melanin, a process called melanization. It is used by many organisms including us !! Its benefits include immune response, thermoregulation etc.

To give you an example, see the below picture of the samples which the authors took from Europe.

Picture1

So, in general as one can see in the Alpine regions where the sunlight is very rare for the whole year, the moths have  less than 20% colouration !! (see, picture above (b))

But why??

It seems that higher melanization limits the amount of other pigments important in the warning signal, thereby setting the stage for atrade-off between defensive signalling and thermoregulation.

The question which the authors looked upon is something like this:

Do variation in male hindwing melanization is linked to thermoregulation and/or involved in a trade-off with protective benefits of colour ?

What did they find?

The authors started off with a combination of field based studies and predation experiments with artificial moths. Have a look at them:

Picture1

  • The amount of melanization increased with increasing latitude in Wood Tiger Moth males from Estonia to north Finland.
  • Individuals in the Alps had a significantly greater amount of melanin covering their hindwings than those in central Finland.
  • Melanization also varied more among individuals in the Alpine region compared with central Finland.
  • Greater melanization also increased the average rate for warming up for the moths.
  • Every 10 per cent increase in the amount of melanin resulted in a 16 per cent increase in the odds of being attacked.

Taken together,the results show the likely existence of a trade-off between thermoregulation and predation risk with respect to the amount of melanin present on the hindwing in Wood Tiger Moths. Specifically, what they found was that greater amounts of melanin in both white and yellow males resulted not only in an increased ability to absorb radiation, but also increased the likelihood of attack by avian predators. The results provide evidence that the differences in costs and benefits of melanin in the two locations can drive phenotypic differences in the warning signal of males on broad and local geographical scales.

Take home message:

If an organism is good at having X, then it must come at some cost. And as X is very costly it does not mean that its not a successful strategy, if the benefits of the costly strategy(X) outweighs the high cost  !!

More on this:

  1. The redder the better: wing color predicts flight performance in monarch butterflies, PLoS One, 2012.
  2. Linking color polymorphism maintenance and speciation, Gray SM, McKinnon JS, TREE, 2007.
  3. Insect melanism: the molecules matter, True JR., TREE, 2003.
  4. Visual predators select for crypticity and polymorphism in virtual prey, Bond AB, Kamil AC., Nature, 2002.