Monday, August 31, 2015

The origin of eukaryotes and the ring of life

The latest issue of Philosophical Transactions of the Royal Society B (Sept. 26, 2015) is devoted to Eukaryotic origins: progress and challenges. There are 16 articles and anyone interested in this subject has to read all of them.

Many (most) of you aren't going to do that so let me try and summarize the problem and the best current ideas on how to solve it. We begin with the introduction to the issue by the editors, Tom Williams, Martin Embley (Williams and Embly, 2015). Here's the abstract ...

A little learning of biochemistry ...

A little learning is a     dangerous thing;
drink deep, or taste not the     Pierian spring:
there shallow draughts     intoxicate the brain,
and drinking largely     sobers us again.
                  Alexander Pope
I've been following Angelo Grasso on Facebook because he posts a lot of biochemistry stuff. His schtick is to post some complicated pathway or structure then marvel at how complex it is and how it had to be designed. For a while I was commenting on his posts in order to show him why his interpretation was wrong or misleading but he just kept posting more examples gleaned from biochemistry textbooks.

This is a classic examples of someone who knows just enough to be dangerous. His latest post is about glycolysis and membrane-associated electron transport in animals. You can see it on the reasonandscience.heavenforum website: Glycolysis. Here's the bottom line ...

Sunday, August 30, 2015

Ten discoveries that would change the way we think about ourselves

New Scientist has published a list of ten ideas that, if true, would change the way we perceive ourselves and our place in the universe [World Turned Upside Down]. I think some of them are pretty good—many of them really would have a profound effect. Of course, some of them are never going to happen and some of them are silly. One of them is already true.

Here they are ...
  1. What if most of reality is hidden?
  2. What if we discover we can see the future?
  3. What if we learn to talk to animals?
  4. What if we are not alone?
  5. What if we don't need bodies?
  6. What if we have no free will?
  7. What if we came from space?
  8. What if intelligence is a dead end?
  9. What if the universe is an illusion?
  10. What if we find god?

IDiots promote twenty-two falsified predictions of Darwin's theory of evolution

Cornelius Hunter is a fellow at the Center for Science and Culture (Discovery Institute). That makes him a card-carrying Intelligent Design Creationist.

He has a website called .DarwinsPredictions.
Charles Darwin presented his theory of evolution in 1859. In the century and half since then our knowledge of the life sciences has increased dramatically. We now know orders of magnitude more than Darwin and his peers knew about biology. And we can compare what science has discovered with what Darwin’s theory expects.

It is not controversial that a great many predictions made by Darwin’s theory of evolution have been found to be false. There is less consensus, however, on how to interpret these falsifications. In logic, when a hypothesis predicts or entails an observation that is discovered to be false, then the hypothesis is concluded to be false. Not so in science.
I was reminded of these "predictions" a few days ago when Casey Luskin interviewed Cornelius Hunter in ID the Future: Casey Luskin and Cornelius Hunter Discuss Darwin's Predictions. I assume that most Sandwalk readers aren't familiar with all these false predictions of Darwinism so here they are with my own brief description.

Friday, August 28, 2015

Jerry Coyne doubles down on his criticism of how evolution is taught in Ontario schools

A few weeks ago, Jerry Coyne got his knickers in a knot because the Ontario school curriculum didn't specifically prescribe the teaching of evolution in the way that he would like [Ontario schools require teaching evolution—except human evolution].

I replied to that post, quoting the Ontario curriculum and pointing out that it was pretty damn good when it comes to evolution [Teaching evolution in Ontario Schools]. The curriculum concentrates on fundamental principles of evolution as they apply to all species. It does not cover any details of the history of life per se. It doesn't specifically mention the evolution of whales, or birds, or any other lineage. It doesn't say which examples have to be included in the classroom instruction. It refers frequently to the fact that humans are not different than any other animals when it comes to biology.

Jerry take this to mean that detailed descriptions of human evolution are specifically excluded and he now claims that this is due to government policy [Ontario school officials respond—or rather, fail to respond—to queries about why they don’t require teaching human evolution].

Human Evolution: Genes, Genealogies and Phylogenies by Graeme Finlay

Human Evolution: Genes, Genealogies and Phylogenies was published in 2013 by Oxford University Press. The author is Graeme Finlay, a cancer researcher at the University of Auckland, Auckland, New Zealand.

I first learned about this book from a book review published in the journal Evolution (Johnson, 2014). It sounded interesting so I bought a copy and read it.

There are four main chapters and each one covers a specific topic related to genomes and function. The topics are: Retroviruses, Transposons, Pseudogenes, and New Genes. There's lots and lots of interesting information in these chapters including an up-to-date summary of co-opted DNA that probably serves a biologically relevant function in our genome. This is the book to buy if you want a good review of the scientific literature on those topics.

Thursday, August 27, 2015

Inside the mind of an Intelligent Design Creationist

The blog Evolution News & Views (sic) is part of the public outreach of The Center for Science and Technology, a subsidiary of the The Discovery Institute.

Ann Guager is a researcher at The Biologic Institute, which is funded by The Discovery Institute. She wrote an article for Evolution News & Views entitled What If People Stopped Believing in Darwin? I think it's safe to assume that this is a common view of a leading Intelligent Design Creationist and close to the position of other members of that cult.

Wednesday, August 26, 2015

Eukaryotic genes come from alphaproteobacteria, cynaobacteria, and two groups of Archaea

Bill Martin and a group of collaborators from several countries have analyzed gene trees from a wide variety of species (Ku et al., 2015). They looked at the phylogenies of 2500 different genes with representatives in both prokaryotes and eukaryotes.

The goal of this massive project was to find out if you could construct reliable consensus trees of prokaryotes and eukaryotes given that lateral gene transfer (LGT)1 is so common.

The results show that LGT is very common in prokaryotes making it quite difficult to identify the evolutionary history of prokaryotic groups based on just a small number of gene trees.

In contrast, eukaryotes appear to be a monophyletic group where all living eukaryotes are descendants of a single ancestral species. There's very little LGT in eukaryotic lineages apart from one major event in algae and plants (see below).

The genes currently found in eukaryotic genomes show that eukaryotes arose from an endosymbiotic event where a primitive alphabacterium fused with a primitive archaebacterium. The remnant of the alphaproteobacterium genome are still present in mitochondria but the majority of the bacterial genes have merged with archaebacterial genes in the nuclear chromosomes. Thus, eukaryotes are hybrids formed from two distantly related prokaryotic species.

A second round of new genes was acquired in eukaryotes when a primitve single-cell species merged with a species of cyanobacterium. The remnant of the cyanobactrial genome is found in chloroplasts but, like the case with alphaproteobacteria, the majority of the cyanobacterial genes merged with other genes in the nuclear genome.

The exact number of trees was 2,585. Among those trees, 49% of eukaryotic genes cluster with proteobacteria, 38% derive from cynaobacterial ancestors, and only 13% come from the archaebacterial ancestor. Thus, it's fair to say that the dominant ancestor of eukaryotes, in terms of genetic contribution, is bacterial, not archaeal.

One of the authors on the paper is James O. McInerney of the National University of Ireland, in Maynooth, County Kildare, Ireland. He made a short video that explains the result.2

1. Also known as horizontal gene transfer (HGT).

2. I hate to contaminate a scientific post by referring to creationists but I can't help but wonder how they explain this data. I'd love it if some Intelligent Design Creationist could describe how this fits in with their understanding of the history of life.

Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F.L., Lockhart, P.J., Bryant, D., Hazkani-Covo, E., McInerney, J.O., Landan, G., Martin, W.F. (2015) Endosymbiotic origin and differential loss of eukaryotic genes. Nature Published online Aug. 19, 2015 [doi: 10.1038/nature14963]

Jesus and Mo

Jesus and Mo, August 26, 2015

Tuesday, August 25, 2015

The apophenia of ENCODE or Pangloss looks at the human genome

This is a paper in French by Casane et al. (2015). Most of you won't be able to read it but the English abstract gives you the gist of the argument. I had to look up "apophenia": "Apophenia has come to imply a universal human tendency to seek patterns in random information, such as gambling."
In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published. The time of hundreds of scientists and hundreds of millions of dollars were not invested in vain since this project had led to an apparent paradigm shift: contrary to the classical view, 80% of the human genome is not junk DNA, but is functional. This hypothesis has been criticized by evolutionary biologists, sometimes eagerly, and detailed refutations have been published in specialized journals with impact factors far below those that published the main contribution of the Encode project to our understanding of genome architecture. In 2014, the Encode consortium released a new batch of articles that neither suggested that 80% of the genome is functional nor commented on the disappearance of their 2012 scientific breakthrough. Unfortunately, by that time many biologists had accepted the idea that 80% of the genome is functional, or at least, that this idea is a valid alternative to the long held evolutionary genetic view that it is not. In order to understand the dynamics of the genome, it is necessary to re-examine the basics of evolutionary genetics because, not only are they well established, they also will allow us to avoid the pitfall of a panglossian interpretation of Encode. Actually, the architecture of the genome and its dynamics are the product of trade-offs between various evolutionary forces, and many structural features are not related to functional properties. In other words, evolution does not produce the best of all worlds, not even the best of all possible worlds, but only one possible world.

Casane, D., Fumey, J., et Laurenti, P. (2015) L’apophénie d’ENCODE ou Pangloss examine le génome humain. Med. Sci. (Paris) 31: 680-686. [doi: 10.1051/medsci/20153106023]

Monday, August 24, 2015

The genealogy of Jesus

I saw this at The Cloisters when I was in New York last week. It's very hard to read1 so I'm not sure if it's accurate.

Here's what the Metropolitan Museum of Art has to say about The Compendium of History through the Genealogy of Christ by Peter of Poitiers.
Admirable for its concision and graphic boldness, this imposing scroll presents a history of the known world from the creation of Adam until the birth of Jesus. It is a teaching tool—a graphic summary of a classroom text. The ancestry of Jesus, traced back to the first man, is shown through a stemma (a system of lines and framed circles that runs down the center of the scroll’s length). Noteworthy ancestors, including King David with his harp, are pictured at regular intervals along the stemma. Successions of biblical rulers, as well as the lineage of ancient rulers of the Near East, Greece, and Rome appear on less elaborate stemmata that diverge from, converge with, and run parallel to that central history.
Sounds authentic to me. I wonder who is listed as the father of Jesus and if the genealogy covers the ancestors of Mary all the way back to Eve?

Peter of Poiters lived in England and the scroll was created in the 1200s. I bet he had lots of fun searching and all the census records from Ur and Egypt.

Here's photo that I took at The Cloisters.

1. It was in a dark corner and my Latin is a bit rusty.

IDiots, suckers, and the octopus genome

The genome of the small octopus, Octopus bimaculoides has recently been sequenced. The results are reported in Nature (Albertin et al., 2015).

The octopus is a cephalopod along with squid and cuttlefish. These groups diverged about 270 million years ago making them more distantly related than humans and platypus. As expected, the octopus genome is similar to other mollusc genomes but also shows some special derived features. Some gene families have been expanded—a feature often found in other genomes.

Sunday, August 23, 2015

Comets and meteorites CAN NOT create a primordial soup in the ocean

I want to talk about two recent press releases on the origin of life.

The first one is from the BBC and it talks about the work of Haruna Sugahara and Koicha Mimura who presented their results at a recent conference [Comet impacts cook up 'soup of life']. They noted that the impact of a comet carrying organic molecules can produce more complex organic molecules.

The second report is from ScienceDaily. It reports a similar study by Furukawa et al. (2015) who examined the idea that the impact of meteorites in the primitive ocean could create more complex organic molecules than those already found in meteors [Meteorite impacts can create DNA building blocks].

What am I doing on my summer vacation?

Here's what I'm doing this summer (right) when I'm not fighting creationists, writing a book, giving talks, playing with the grandchildren, and visiting exotic cities in Canada and the United States.

I built the main part of the patio twenty years ago. I recall working on it for 6-8 hours at a stretch but today I'm pooped after three hours.

I think the stones have gotten heavier.

How do Intelligent Design Creationists deal with pseudogenes and false claims?

Some of the people who comment here have pointed out that this is the second anniversary of a post by Jonathan McLatchie on Evolution News & Views (sic): A Simple Proposed Model For Function of the Human Vitamin C GULO Pseudogene.

That post is significant for several reasons. Let's review a bit of background.

Intelligent Design Creationists have a problem with pseudogenes. Recall that pseudogenes are stretches of DNA that resemble a gene but they appear to be non-functional because they have acquired disruptive mutations, or because they were never functional to begin with (e.g. processed pseudogenes). All genomes contain pseudogenes. The human genome has more than 15,000 recognizable pseudogenes.1 This is not what you would expect from an intelligent designer so the ID crowd tries to rationalize the existence of pseudogenes by proposing that they have an unknown function.