The Daft Designer Does It Again

Cellular defense against latent colonization foiled by human cytomegalovirus UL138 protein | Science Advances

Here's a little challenge to Michael Behe and his chums from the Discovery Institute.

No, it's not to explain how it came about because that's too easy. It's to explain why it came about. The problem is not that it is irreducibly complex but that it is irredeemably stupid.

Here's the situation:

A family of viruses, the herpesviruses, has a mechanism for overcoming the human immune system when it infects cells. It basically hides inside the cell nucleus looking for all the world like part of the normal genome and only in certain situations does it come out of hiding, start replicating and

Why Science Works - Doing It Like Adults

The basic difference between science and religion is that science is grown up while religion is essentially childish. This is illustrated by a controversy which has suddenly blown up in a fairly obscure but nonetheless interesting aspect of evolutionary biology in the last week.

An interesting paper was published a few days ago which seemed to show that horizontal gene transfer (HGT) may account for up to 18% of the tardigrade ('water bear') genome, suggesting that HGT could have played a bigger role in the evolution of multicellular organisms than is generally recognised.

HGT is widely suspected to have played a part in the evolution of prokaryote cells so that acquiring genes evolved in another species could have been a short-cut to evolution or a way for new combinations of genes to come together, analogous to sexual reproduction. In eukaryote cells, the incorporation of prokaryotes was a form of HGT after all, but for HGT to have played a wider role in the evolution of multicellular species would be surprising - hence the interest in this paper and why I wrote about it.

Now, however, another group has published a paper which suggests that the result of the genome analysis may have been an artifact produced by contamination:

How Evolution Gave Us Grannies

Human-specific derived alleles of CD33 and other genes protect against postreproductive cognitive decline

There's something special about a granny. Granddads are special too of course, but not quite like a granny. Ask my grandchildren.

Grandparents are biologically, on the face of it, a little bit of a mystery especially in a social species and especially in one like humans where for most people for most of the time until the discovery of agriculture, life consisted mostly of hunting and gathering food. Anyone not capable of joining in would have been a drain on the resources of those who could so it seems logical to suppose that any process which removed surplus people from the group after their fertile and productive years were over would be advantageous to the group and so would be expected to evolve. In fact, when you look at our closest relatives, chimpanzees, you find that the females tend to die soon after their fertility ceases.

Creationism's Big Problem

Otago researchers describe new North Pacific fossil whale, News at Otago, University of Otago, New Zealand.

This week's 'missing' transitional fossil is a new species of baleen whale which lived in what is now the North Pacific, 30 - 33 million years ago. It shows distinct evidence of transition between the toothed and the baleen whales.

Fucaia buelli is described in a paper published today in Royal Society Open Science by Ewan Fordyce and Cheng-Hsiu Tsa of the University of Otago, New Zealand and Dr Felix Marx of Museum Victoria, Melbourne, Victoria, Australia.

The Blue Tarantulas and the Stupid Designer

Singapore Blue Tarantula (Lampropelma violaceopes)

Source: Wikipedia

Blue reflectance in tarantulas is evolutionarily conserved despite nanostructural diversity | Science Advances

Imagine you're, say, a manufacturer of refrigerators and you've employed a designer to modernise your range. The basic technology is fine - things like the heat-exchange unit, door switch that turns the light on and off - and all you need is some styling to give your range more appeal in the prevailing market.

Now, what would you think if you found this designer was redesigning the heat exchanger or the coolant pump, not to make it any better - in fact some of his designs are worse than the ones you normally use - but because it hadn't occurred to him to use the ones you have in stock. In fact, he didn't know they had ever been designed before.

Northern Ireland - Catching Up On Human Rights

NI abortion law 'breaches human rights' | BBC News

In another example of how secular humanism is replacing archaic Christian bigotry and judgmentalism, the Northern Ireland High Court in Belfast has ruled that the Northern Ireland Abortion Laws, which differ markedly from those in the rest of the United Kingdom, are in breach of fundamental human rights.

Human rights, of course, come from the concept of maximising individual liberty, freedom of choice, freedom of conscience, equality before the Law and

Ashyxiated Whales Show Evolution In Progress

A: external view of sole’s tail hanging out of blowhole. B: blowhole cut open to the right side, revealing the sole in the vestibular sac. The white arrow indicates the left side of the blowhole opening, while the red arrow indicates the fish’s tail in both images.*

Source: doi:10.1371/journal.pone.0141951.g001

PLOS ONE: Fatal Asphyxiation in Two Long-Finned Pilot Whales (Globicephala melas) Caused by Common Soles (Solea solea)

A sad report published in PLOS ONE serves to illustrate the interaction between a species and its environment and poses a neat little question for those who still doubt that Darwinian Evolution by natural selection is the mechanism of adaptive change in a species.

Long-finned pilot whales (Globicephala melas) normally live and hunt in North Atlantic, living on squid and other cephalopods and only rarely venture into the shallower North Sea. However, for reasons which may be related to the death from disease of one of the pod - a female - who may have become disorientated and led her extended family the wrong way (pods of pilot whales are known to stay close to a sick member) - a pod of 30-40 of these whales found their way into the North Sea in November 2014.

Six weeks later a decomposed long-finned pilot whale was found washed up on the Belgian coast. A post mortem found a flatfish, a common sole (Solea solea), stuck in the blowhole of the dead whale. Three weeks later another dead long-finned pilot whale was found with another common sole stuck in its blowhole. The strong probability is that both these whales were asphyxiated by these flatfish.

Does God Prefer Bats?

The evolution of bat nucleic acid-sensing Toll-like receptors - Escalera-Zamudio - 2015 - Molecular Ecology - Wiley Online Library

Here is today's embarrassing question for creationists. Does your hypothetical intelligent designer favour bats and hate the rest of us?

The reason you need to answer this is because a paper published today shows that bats have a better immune system than other mammals. I'm assuming that creationists only believe in one intelligent designer and not millions of competing intelligent designers all closely guarding their designs and refusing to share.

Drunken Catholic Monks Abused Minnesota School Boys

The Rev. Finian McDonald. "More than 200 victims."

Minnesota Star Tribune

The Rev. Finian McDonald. "More than 200 victims."

Source: Minnesota Star Tribune

Records reveal Minnesota priests raped hundreds of kids for decades — and church buried the evidence

Records released under court order last Tuesday give a glimpse of the extent of the institutionalised child abuse and cover-up by Catholic priests over a 20 year period at a private boys preparatory school run by monks from the St. John’s Abbey in Collegeville, Minnesota.

The order was granted by the judge as a result of an action brought by one of the victims. This is the first time the monastery has released any information relevant to these claims despite being embroiled in lawsuits for some 20 years. The papers only relate to five priests. Papers relating to allegations against a further fourteen priests have yet to be released.

One of the accused is Rev. Finian McDonald who has confessed to drinking heavily and preying on more than 200 victims, even traveling to Thailand to molest male child prostitutes as young as 13. The other four are Rev. Tom Gillespie, former priest Francis Hoefgen, the late Rev. Bruce Wollmering and the late Rev. Richard Eckroth. Earlier this year, Hoefgen was acquitted on a specific charge of sexually harassing a teenage boy but the released records show a pattern of predatory behaviour from the 1980s onwards.

Tardigrades Shock For Creatards

Inside the Bizarre Genome of the World’s Toughest Animal

If you want good evidence of the common origins of living organisms on Earth, it would be difficult to find anything better than the tardigrades or water bears.

These strange little creatures live just about everywhere on Earth from mountain tops to ocean depths, from hot springs to polar ice. They will even be found living in your guttering, and they are almost indestructible. They are so different to other creatures that they are given a phylum all of their own, the Tardigrada. There are something like 1,150 different species.

They survive long periods of extremely inhospitable conditions by withdrawing all their appendages inside

Evolution Is Winning The Battle In USA

Majority of Unaffiliated Believe Evolution Occurred Through Natural Processes | Pew Research Center

We're in the End Times. The signs are unmistakable. Any day now, real soon...

The End-times for religious fundamentalism in America, that is. There are now clear and unmistakable signs that the battle in the USA between scientific evolution and biblical creationism is being won by science, and, if Europe is anything to go by, religion in the USA is standing on the brink and staring into the abyss.

Firstly, there was the Pew Research Centre survey into Americans, Politics and Science Issues published on 1st July 2015 from which the chart on the right is taken. This shows how acceptance of evolution has recently shown significant upswing in a year, having been almost static for the previous five. The movement is not large in absolute terms, from about 61 to 65% but this is far larger than anything recorded over the previous five years. There is also a corresponding downward swing in the proportion of people who believe in creationism.

Idiot Design - Why Mice Have Longer Sperms Than Elephants

Honestly! They are THAT big!

Sperm number trumps sperm size in mammalian ejaculate evolution | Proceedings of the Royal Society of London B.

When it comes to sperm, size does matter, but bigger is not always better.

In fact, according to a paper published by a University of Zurich team and published in the Royal Society of London Proceedings B, the bigger the species the better it is to have small sperms while the smaller the species, the better are sperms with big tails. Better, of course, being defined as being better able to find and fertilise the egg.

There are couple of reasons for this, one of which is

"God Hates Humans!" Winning The Antibiotic Arms Race

Escherichia coli

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study - The Lancet Infectious Diseases.

Creationists and especially the 'Intelligent Design' version, have some serious explaining to do.

Although they habitually try to hide the fact that creationism has a politico-religious agenda by pretending it is some sort of valid alternative science, to a person they are religious fundamentalists, usually Young Earth loons, and invariably oppose secularism and try to dismantle the 'wall of separation' which secular nations build between church and state. So, to assume they believe in a benevolent, anthropophilic

Ancient Teeth Show Human Roots

Reconstruction of a Neanderthal woman

Source: PLOS Biology

Nuclear and mitochondrial DNA sequences from two Denisovan individuals | PNAS

If the name Svante Pääbo doesn't strike fear into the heart of creationist frauds they haven't done enough reading.

Svante Pääbo heads up the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany which has perfected the art of DNA recovery and is producing masses of DNA data and analysis showing how the modern human species , Homo sapiens, not only evolved but how we interbred with related species as we initially diverged, especially out of Africa. Pääbo's team were the first to extract Neanderthal DNA and to show how non-African H. sapiens have around 4% of Neanderthal DNA and thus must have interbred with them when we migrated out of Africa and found an ancient population of H. neanderthalensis already in Eurasia.

They also isolated DNA from a finger bone found in the Denisova Cave in the Altai Mountains of Siberia and showed that a third species of Homo, related to but distinct from Neanderthals, co-existed in East Asia with both us and Neanderthals and contributed a variable amount of their DNA to the H. sapiens of Southeast Asia and Oceania.

Mormon Cult Losing Members Over Homophobic Bullying

Thousands To Quit Mormon Church Over New Anti-Gay Decree – Public Mass Resignation Event Saturday - The New Civil Rights Movement

News that thousands of Mormons are planning to leave the cult in protest at its decision to increase the persecution of homosexuals is evidence that the Mormon cult, like other churches, is struggling to keep up with the penetration of humanist values into society.

Like the Catholic Church which is haemorrhaging members in the developed world over it's persecution

No More Arguments - Birds Are Modern Dinosaurs

Bird embryos uncover homology and evolution of the dinosaur ankle : Nature Communications : Nature Publishing Group

Science is like a detective story. You accumulate evidence, examine it and let it lead you to the truth. But in that body of evidence there may be a few little pieces that seem to be pointing to a different truth or to falsify the truth that everything else seems to be pointing to. The question is, how strong is this little bit of contrary evidence? Can the overall conclusion live with it or is it fatal so that some other truth has to be found to accommodate it and all the other evidence?

Often, the problem can be solved by a closer reassessment of this evidence. Things look very different under a microscope.

Jumping Genes Jump All Over Creationism

Source: Aurélien J. Doucet et al.
A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition.
Molecular Cell, November 2015 DOI: 10.1016/j.molcel.2015.10.012

Copyright © 2015 Elsevier Inc. All rights reserved.

Grabbing a parasite by the tail: Team solves 'jumping gene' mystery: First demonstration of the poly(A) tail's key role in LINE-1 retrotransposition -- ScienceDaily

Here's a conundrum for creationists.

What intelligent purpose could there possibly be for creating short pieces of DNA that randomly cause genetic diseases such as haemophilia, Duchenne muscular dystrophy, and cancer by randomly jumping from one location to another in our genome and sometimes landing in the middle of an essential gene causing it to mutate?

I can only think of two reasons, if you can call the second one a reason. Malevolent intent or mindlessness. Perhaps a creationist can suggest a benevolent reason for it because I can think of none whatsoever.

Apparently, these short 'jumping' genes come in two forms. Both need a 'tail' of a short stretch of multiple copies of adenosine (poly(A)) so that a protein called ORF2p can attach

My Books - What The Critics Say

I love Amazon's book reviews. Basically, anyone can say anything they want. Fortunately, there is a check that they've bought the book (a verified purchase) but anyone can write anything they want, truth or lies, accurate or inaccurate. Even semi-literate creationist trolls are free to post their abuse apparently with impunity.

Despite that though, and I'm fairly sure most of these people have actually bought or read the books, there are some really flattering reviews.

From Amazon UK

• Excellent tonic for the rational. (Amazon Customer, verified purchase)
• Well written if a little heavy going for someone like me. If you've enjoyed Rosa's blog postings over the years you'll enjoy this with a mix of new articles and some older ones that have been updated. (Wulf)
• Garbage. A compilation of bullocks from his blog written under a fake name that you can google for free if you want to waste your time. (Timothy - ie Timothy Kerchner, Tiny Tim the habitual Internet abuser and creationist.)
• Bought for husband - he hasn't put it down since it arrived - looks like other volumes will be excellent Christmas present - if he can wait that long ! (Mrs J Busby)

Religious 'Nones' Quickly Becoming Less Religious

Religious 'nones' becoming more secular | Pew Research Center

More signs of the growing penetration of secular Atheism into that bastion of Christian fundamentalism, the USA, was published today by the Pew Research Center. One wonders if there will ever again be an honest survey which is good news for religion. It has been relentlessly bad news for about the last 50 years and seems to be getting much worse.

Recent surveys have tended to concentrate not so much on the growth of Atheism in America per se but in the growth on 'nones' as a proportion of the population and consequent decline in the proportion of groups such as Catholics, Episcopalian, Baptist and other Protestants, etc.

Several people have rightly pointed out that 'none' is not the same as Atheist and that many 'nones' remain religious, some deeply so. It simply means anyone who doesn't self-identify as affiliated to any particular faith or denomination.

The Power Of Magical Thinking

Believing What We Do Not Believe: Acquiescence to Superstitious Beliefs and Other Powerful Intuitions | PsycNET

How do religious people manage to hold two mutually exclusive view simultaneously?

How for example, does someone like Francis Collins, former head of the Human Genome Project and passionate advocate for evolution on an old Earth in an older Universe, whose entire academic career depended on his understanding and acceptance of the role of DNA in evolution, still manage to believe he needs to beg forgiveness because he inherited the 'sin' of a founding pair of humans who were made by magic a few thousand years ago?