I recently stumbled on a paper with an intriguing title" "Sixty years of genome biology" (Doolittle et al., 2013). It celebrates the 60th anniversary of the Watson & Crick paper on the structure of DNA. The editors of Genome Biology describe key advances in genome biology.
Introns
Several editors (Graveley, Ule, Henikoff, Doolittle) said that the discovery of "genes in pieces" was a very significant advance in genome biology in the past sixty years. You can't argue with that.
Restriction Mapping
George Weinstock counts restriction mapping as a key advance. I understand his point since the development of restriction mapping gave us maps of the actual structure of the genome for the first time (genetic maps are imprecise and depend on the presence of mutations).
A new regulatory paradigm: micoRNA
John Rinn, who coincidentally works on small RNAs thinks this is a significant advance in genomics. I don't agree.
The original 'data explosion': microarrays
Alicia Oshlack is an astrophysicist who got into genomics through bioinformatics and the analysis of microarray data. Microarrays are important in genomics and should be included in any list of significant advances as long as the list includes technological advances.
Michael Schatz says, "The most significant advance in genome biology since 25 April 1953 has been the rise of large-scale DNA sequencing ...." He is correct, if technologies are to be included in the list.
'Sequence is power': the human and mouse genome projects
Chris Ponting, Mark Gerstein, and Peter Fraser think that the publication of the human genome sequence is the most significant advance in genome biology. I suppose it depends on what you want to know about genomes. If your focus is on humans and medicine then, obviously, the sequence of the human genome is important. I thought the sequences of the yeast, nematode, and Drosophila genomes were pretty exciting and so were the sequences of bacterial genomes.
Retelling the human story: analysis of ancient and historical DNA
The is Detlef Weigel's contribution.
The exception to the rule: lateral gene transfer
Curtis Huttenhower thinks that the discovery of lateral gene transfer is "one of the most remarkable [discoveries] in the history of genome biology."
Nobody mentioned junk DNA and the resolution of the C-value paradox. Nobody mentioned the small number of genes in the human genome in spite of the fact that a great many articles begin with the claim that this was a shocking discovery [but see False History and the Number of Genes]. Jernej Ule mentioned alternative splicing but nobody else did in spite of the fact that many papers claim that most human genes are capable of making several different proteins. This is also a false claim, IMHO, but you'd never know that from reading the journal. Peter Fraser was the only one who mentioned the vast regulatory network of enhancers as claimed by the ENCODE Consortium. If true, that would clearly count as a major discovery. (It's not true.) Eukaryotic genomes are chock full of defective transposons but none of the editors thought that was a key advance in our understanding of the genome.
Doolittle, W.F., Fraser, P., Gerstein, M.B., Graveley, B.R., Henikoff, S., Huttenhower, C., Oshlack, A., Ponting, C.P., Rinn, J.L., Schatz, M., Ule, J., Weigel, D., and Weinstock, G.M. (2013) Sixty years of genome biology. Genome Biol, 14(4), 113. [doi: 10.1186/gb-2013-14-4-113]
Eukaryotes are the descendants of a fusion event where a primitive archaebacterium fused with a primitive alphaproteobacterium. Over time, the genome of the alphaproteobacterium became reduced as many of its genes were transferred to the genome of the other partner. Today, the remnant of the alphaproteobacterium is the mitochondrion and the remnant of the archaebacterium has become the nucleus.
The human mitochondrial genome is a small circular genome of 16,570 ± 50 bp (Rubino et al., 2012). It contains only a few genes but it is still invading the nuclear genome. The average human genome contains about 600 fragments of mitochondrial DNA ranging in size from 30 bp to almost the full size of the mitochondrial genome (Simone et al. 2011). They are called NumtS or nuclear mitochondrial sequences. 1
Some of the genome inserts are 100% identical in sequence to the standard mitochondrial genome sequence indicating a recent colonization event. Others are as little as 63% identical, the cut-off similarity. The total amount of mitochondria-derived DNA in one individual was 627,410 bp amounting to only 0.02% of the genome (Simone et al., 2011).
Constructive Neutral Evolution (CNE) is a term that describes the evolution of complex systems by non-adaptive mechanisms. The idea (and the name) was developed by Arlin Soltzfus in 1999 (Stoltzfus, 1999) but it has antecedents in the literature and in the environment where Stoltzfus did his post-doc (Michael Gray and Ford Doolittle). It has been promoted by a number of prominent evolutionary biologists/population geneticists, notably Michael Lynch in his book The Origins of Genome architecture. Several examples have been described and discussed in the scientific literature and in popular books. For example, there is good reason to think that the evolution of the complex spliceosome that removes introns has evolved by mainly non-adaptive evolution.
Ford Doolittle and Michael Gray are fans of constructive neutral evolution. They and their collaborators wrote a review of the idea in Science (Gray et al., 2010). It has the provocative title "Irremediable Complexity." The same authors (different order) published another review the following year (Lukeš et al., 2011).
It's important to understand this concept because it challenges the idea that the evolution of complexity is adaptive and it sets the stage for challenging the idea that all adaptive structures arose exclusively by natural selection. Almost everyone who writes about constructive neutral evolution understands that it poses a problem for those who cling to adapatationist or selectionist views of evolution. It also helps us understand why the core idea behind irreducible complexity has been refuted.
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.
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.
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.
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.
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 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 PopeI'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 ...
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.
Cornelius Hunter is a fellow at the Center for Science and Culture (Discovery Institute). That makes him a card-carrying Intelligent Design Creationist.
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.
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.
Human Evolution: Genes, Genealogies and Phylogenies was published in 2013 by Cambridge 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.
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.
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]
