Friday, September 04, 2015

Jim Lake and the Eocyte tree

I met James (Jim) Lake for the first time more than 20 years ago but I had a chance to talk to him more recently in Chicago in 2013 [People I Met in Chicago at SMBE2013].

He became famous (infamous?) for challenging the Three Domain Hypothesis of Carl Woese (and friends) and for advocating better methods of constructing gene trees. Jim Lake proposed that eukaryote nuclei arose from within the archaebacterial clade and not as a sister groups of Archaea as the Three Domain Hypothesis claimed. The sister group was the "eocytes," represented at the time by Sulfolobus solfataricus, an archaebacterium that lives in hot springs (~80°C) and uses sulfur as a source of energy.

Tuesday, September 01, 2015

Debating Darwin's Doubt: the prequel

I've had a chance to read most of Debating Darwin's Doubt and, as I mentioned earlier today, it doesn't address any of my criticisms. Here's the list of my blog posts ...
I'm really jealous because the IDiots spend a lot of time on Nick Matzke's blog post and on other posts.

I can only assume that they have no rebuttal. I know they read my blog and they should have been on the look-out for my critique in September 2013 because David Klinghoffer specifically challenged me to review Darwin's Doubt.1 [On Darwin's Doubt, Still Waiting to Hear from Big Shots in the Darwin Brigade]. Here's what he said on September 4, 2013 just before I put up those posts.

On spelling names correctly ... and irony

David Klinghoffer was recently aroused by a comment from me that was published on the Forbes website [Meet The Canadian Scientist Who Loves Battling American Creationists]. I said ...
Most scientists and science lovers cannot win a debate with the best intelligent design creationists ... That's because their knowledge of science is nowhere near as good as they think it is. One of the other reasons for debating creationists on my blog is to educate the non-creationists. I spend almost as much time criticizing fellow scientists as I do attacking creationists.
Naturally, David Klinghoffer thinks I was referring to him [University of Toronto Biochemist Admits Most ID Critics Can't Win a Debate with Us].

For the record, I don't think that David Klinghoffer is one of the best Intelligent Design Creationists. However, I stand by that statement as long as you understand that it refers to genuine debates.

Later on in his post, Klinghoffer criticizes me for spelling Ann Gauger's name incorrectly in one of the times I referred to her in a recent post. I corrected that typo. (I accidentally wrote "Guager.")

Klinghoffer refers to me as Lawrence Moran but my first name is spelled Laurence. (He can call me "Larry" if it's too difficult to spell Laurence correctly.) I note that he also spells my first name incorrectly in Debating Darwin's Doubt. (David Klinghoffer is the editor of that book.)

Klinghoffer adds ...
Leave aside the gratuitous reference to creationism, which Moran knows perfectly well that we don't advocate [see photo above] if he reads us as regularly as he seems to do [I do read them accurately, that's the problem], and if words have any meaning [the word "creationist" has meaning and Klinghoffer is a creationist]. Give him credit, though, for accuracy on this point: Most ID critics could not stand up in an encounter with an ID advocate like Meyer. You're right! I agree. They couldn't. Could you, Dr. Moran? That's something I'd love to see.
Well, David, you just might get your chance.

As you know, I posted a number of articles critical of Stephen Meyer's book Darwin's Doubt. Now that I have a copy of the book you edited, Debating Darwin's Doubt, I'm looking forward to all the rebuttals of my arguments that you included in that book. Here are my posts, in case you forgot.
Oops, my quick scan of the book failed to find any mention of any of those blog posts! Damn. I guess Stephen Meyer and his creationist buddies are waiting for Debating Darwin's Doubt: Part Deux in order to address my criticisms. I'm a little miffed though, because the book tries to rebut other blog posts and it even addresses a different blog post of mine.

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 Culture, a subsidiary of the The Discovery Institute.

Ann Gauger 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.