Archive for the 'Biology' Category
Take a Ford and a Chevrolet, two automobiles that were intelligently designed. Now, try to take the engine from the Ford and put it in a Chevrolet. Does it fit? Can it be used? The answer is no. How about the door handle? The answer is no again. How about the headlight? The answer is no again. In this example, intelligent design does not result in interchangeable parts.
Now, take a human and a yeast. Take a human gene and put it in a yeast. Does it fit? Can it be used? The answer is yes. A quick search of google.com for “human yeast complementation” results in many examples of human genes complementing yeast genes and vice versa.
How can a yeast gene work in a human? It works ecause yeasts and humans are descended from a common ancestor, through evolution, and are not designed by an intelligence.
And I hope this is all I’ll ever say about this topic.
May 29 2008 | Biology | Comments Off
Martin et al. published a paper, “The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis”, in the 06 March 2008 issue of Nature. The paper (PubMed record) is accompanied by a News and Views article, “Fungal symbiosis unearthed”, by Dan Cullen of the USDA Forest Products Laboratory in Madison, Wisconsin. (A subscription to Nature is required to obtain electronic copies of the paper and the article.)
Fungi and plants enter a symbiotic relationship in which the microrrhizae of fungi join with the roots of plants, allowing an exchange of nutrients between the organisms. Plants transfer simple carbohydrates, the products of photosynthesis, to the fungi, and they receive in return water and minerals, including ammonia and phosphate ions.
The researchers identified approximately 21,000 genes in the 65 million base pair genome; about 70% of the predicted genes have significant similarity to genes in the sequence databases. As might be expected, the number of predicted membrane-bound transporter proteins is large.
The authors of the paper and Dr. Cullen in his commentary noted that it was expected that the L. bicolor genome would contain genes encoding enzymes for breaking down cellulose and lignin. It was surprising, therefore, that only one gene encoding an endoglucanase with a cellulose-binding domain was identified, and no genes encoding enzymes for breaking down cellulose were found. In contrast, a large number of genes predicted to encode lipases and proteinases were identified, suggesting that L. bicolor derives nutrients from the degradation of bacteria and invertebrates. Martin et al. write:
These observations suggest that the inventory of L. bicolor plant cell wall-degrading enzymes underwent massive gene loss as a result of its adaptation to a symbiotic lifestyle, and that this species is now unable to use many plant cell wall polysaccharides as a carbon source, including those found in soil and leaf litter.
Having now in hand this fungal genome and the genome of the black cottonwood, Populus trichocarpa, which enters into ectomycorrhizal symbiosis, the authors predict it will be much easier to identify the genes that mediate the symbiotic relationship.
March 18 2008 | Biology | Comments Off
On 04 March 2008 I wrote a post about the personal genome. In the days since that post, I have expanded my reading about this topic, and I have found two blogs that cover personal genomes/personalized medicine very well.
The first is Gene Sherpas, a blog by Steve Murphy, M.D., about “personalized medicine and you.”
To usher in the new paradigm of personalized medicine we will need to travel a perilous path. Much like the route through the Himalayas it has punished the naive and self-reliant. That is why I have dedicated my life to being a Gene Sherpa. What is a gene sherpa? The Sherpa speaks the language of the trail, he/she knows short cuts and dangerous paths to avoid. This blog is for those wishing to take the journey and those wishing to become Gene Sherpas. Interested? Email me…
Dr. Murphy also writes:
I am the founder of a Personalized Medicine practice (likely the first private practice of its kind). In addition I am the Clinical Genetics Fellow at Yale University until 2010. Now not under contract and that’s why I am posting and running my practice. I also am developing a modern medical genetics curriculum for residents and other physicians. On this blog I am educating the public and hopefully some physicians about the field of genetics and personalized medicine.
The Gene Sherpas blog contains many informative and provocative posts, including a recent post about twin studies and how identical twins aren’t actually so identical when DNA methylation and copy number variation are taken into account.
From Gene Sherpas, I learned about Misha Angrist’s GenomeBoy blog. Dr. Angrist earned a Ph.D. in Genetics at Case Western Reserve University, and he now writes about personal genomics. Dr. Angrist writes:
I work as the Science Editor for the Duke University Institute for Genome Sciences & Policy (although this site and its content are my own). In 2007 I became the fourth subject in Harvard geneticist George Church’s Personal Genome Project. As the PGP moves forward, I am chronicling the dawn of personal genomics, that is, people obtaining their genomic information for whatever reason(s) and figuring out what to do with it. I am interested in the relevant technologies and especially the attendant privacy and other ethical/legal/social issues.
Dr. Angrist posts frequently about his participation in the Personal Genome Project and about the rapid technological advances that will make personal genomes easy to obtain in the near future.
March 17 2008 | Biology | 1 Comment »
Today I read “Understanding Evolutionary Trees”, by T. Ryan Gregory, the author of the Genomicron blog. Dr. Gregory mentioned his paper in his blog post, “Evolutionary Trees for Darwin Day”, and the paper appears in the new journal Evolution: Education and Outreach, which is free online through 2008.
Nimravid posted a summary, which was graciously acknowledged today by Dr. Gregory, and that was how I learned about the paper. Nimravid’s summary is good (as are all of Nimravid’s posts), but I recommend reading the entire paper, which is very readable and well-presented. I found that I have a pretty clear idea of how to interpret evolutionary trees, but I learned the differences in the terms dendrogram, cladogram, and phylogram.
Dr. Gregory makes an important point in his paper:
[I]t is impossible to know with certainty that any given phylogeny is historically accurate. As a result, any reconstructed phylogenetic tree is a hypothesis about relationships and patterns of branching and thus is subject to further testing and revision with the analysis of additional data.
In my mind, this is why evolution is a science. An evolutionary tree is a model of the evolutionary relationships among organisms. A good model is consistent with existing observations, and it provides a hypothesis than can be tested as additional data are gathered. If the model is inconsistent with the new data, the model is revised and subjected to testing with even more data.
March 16 2008 | Biology | Comments Off
I learned about the Free Rice web site today. The object is to “learn free vocabulary and give free rice.”
The premise is simple. The site presents a word and four possible meanings, and you click on the meaning you think is correct. With each correct guess, you earn 20 grains of rice that the site owner donates to the United Nations World Food Program. Advertisers pay to display ads on the site, so they are the ones who ultimately pay for the donated rice. The game is fun and addictive, and it has the benefit that you can learn some new words.
As a scientist, I have a pretty large vocabulary, so I can reach a vocabulary score of 48. My wife, who edits medical textbooks and consequently has an enormous vocabulary, routinely reaches 53. A score of 55 is the highest possible.
I have learned some new words, some useful and some not. When someone mentions they wore a rebato trimmed with vair, now I know what they’re talking about.
But one of the words hit my hot button. The word was nostoc, and the required answer was blue-green alga. This annoys me because it is like calling a dolphin a fish, a mushroom a plant, or water an element. The answer is incorrect.
What were once called blue-green algae are properly called cyanobacteria. The distinction is important, because cyanobacteria are prokaryotic organisms and algae are eukaryotic organisms.
While I’m ranting: It’s one alga, many algae; one bacterium, many bacteria.
March 09 2008 | Biology and Internet | Comments Off
This is already old news, but in this week’s issue of Science, Gibson et al. published their paper on the synthesis of a genome of Mycoplasma genitalium. (Sometimes I just have to wait for a physical copy of the journal to arrive before I have time to read a paper.) This work was performed at the J. Craig Venter Institute (JCVI) in Rockville, Maryland. A special commentary in the Perspectives section, “Reconstruction of the Genomes”, was written by Drew Endy, who is Assistant Professor in the Biological Engineering Department at MIT. (A subscription to Science is required to read the paper and the commentary.)
The paper was originally published online on 24 January 2008, at which time there was a lot of coverage in the press and in blogs. For example, see “Synthetic Genome: Signed, Sealed, Decoded”, by Andrew Pollack of the New York Times, and a roundup of coverage of the announcement at blog.bioethics.net. This paper was also the topic of Science Friday on 25 January 2008.
While the assembly of this synthetic genome is without a doubt a significant technical achievement, the paper does not reveal whether the genome can be transplanted into a bacterial cell. This makes the result anticlimactic; it was like reading about the building of a new airplane, with lots of description about the design of the wings and how the rivets had to be placed just so, but without a demonstration that the airplane could actually fly. I suspect strongly that the transplantation was attempted (several times) without success.
The same group has shown that it is indeed possible to transplant a genome from one bacterial species to another, as described in a paper in Science by Lartigue et al. We must now wait for the JCVI to get their airplane off the ground.
March 05 2008 | Biology | Comments Off
We are on the verge of being able to have our genomes sequenced and analyzed. Today in the article “Gene Map Becomes a Luxury Item”, by Amy Harmon of the New York Times, Ms. Harmon describes how wealthy people are beginning to sign up to have their genomes sequenced and analyzed by Harvard Professor George M. Church’s company Knome at a price starting at $350,000. (Knome is pronounced “know me”, and the company’s web site proclaims “know thyself”, a play on the company’s name.)
University of California—Davis Professor Jonathan A. Eisen, on his The Tree of Life blog, jokingly complained that Ms. Harmon had interviewed him but had discarded his quotes. Ms. Harmon, good sport that she is, responded in the comments by contributing outtakes of the article that included discarded quotes from Dr. Eisen and from J. Craig Venter.
Dr. Venter, of course, has already had his genome sequenced and analyzed by his institute, the J. Craig Venter Institute in Rockville, Maryland. The paper describing Dr. Venter’s genome was published in PLoS Biology. Dr. Venter has written a book, A Life Decoded: My Genome: My Life, and a good review is available on Dr. Jonathan Badger’s T. taxus blog.
Dr. James Watson, one of the co-discoverers of the structure of DNA, has had his genome sequenced; the data are available at the James Watson’s Personal Genome Sequence Browser web site at Cold Spring Harbor Laboratory.
Dr. Church has also organized the Personal Genome Project. This project will sequence and analyze the genomes of volunteers, who will share their medical records, making the data much more useful. I wrote eight days ago about the 1000 Genomes Project, for which medical records will not be available. A blog about the Personal Genome Project, named The Personal Genome, is written by Jason Bobe.
Another company that is providing personal genome data is 23andMe, which provides a blog named The Spittoon. For about $1000, 23andMe obtains data on nearly 600,000 single nucleotide polymorphisms (SNPs) and provides a genetic analysis of the data. Andrew Scheidecker had his genome analyzed by 23andMe in December, 2007, and wrote software called Personal Genome Explorer that made his data available to everyone.
The goal of inexpensively obtaining a genome analysis was deemed important enough for the Archon X Prize for Genomics to promise an award of $10 million for the successful sequencing of 100 genomes in 10 days at a cost of less than $10,000 per genome. See “$10 Million Prize Set Up for Speedy DNA Decoding”, by Nicholas Wade of The New York Times.
Other companies that have developed high-throughput sequencing technologies that might make the relatively inexpensive genome within reach are 454 Life Sciences, Helicos BioSciences, and Pacific Biosciences. Dr. Eisen saw a talk about the Pacific Biosciences technology and came away enthusiastic, writing in his blog:
But it was the last talk of the whole meeting that really did blow my mind. It was from Steve Turner from Pacific Biosciences. He presented an overview of their sequencing technology as well as a tiny bit of data. Now, normally I am uninterested in marketing talks where little data is presented. But this talk was different. First, their technology clearly has enormous potential for revolutionizing the sequencing field. Basically, what they are doing is reading the activity of a DNA polymerase as it replicates a single DNA molecule and they do it in real time. He referred to this as using the DNA polymerase as a sequencing engine and then he took the crowd through the details of the technology and some of the modifications they have made to make it work better.
Ms. Harmon’s article is one of a series in the New York Times named The DNA Age; another good article written by Ms. Harmon is My Genome, Myself: Seeking Clues in DNA. Other good articles at the New York Times on personal genomes and high throughput sequence are “The Race to Read Genomes on a Shoestring, Relatively Speaking” and “Working by Eavesdropping on DNA Doing Its Work”, both by Andrew Pollack.
In a few years, it will be routine for everyone to have their genome sequenced and analyzed. It will take a long time to get the quality of the predictions up to a useful level, however. How much of the genome needs to be sequenced to obtain an accurate analysis, 600,000 SNPs (23andMe) or the full genome (Knome, Personal Genome Project)? I personally am interested in having my genome analyzed because, as a scientist, I am always interested in data. However, I would consider the genetic analysis to be speculative until many more genomes have been analyzed.
Notes added on 6 March 2008:
The Genetic Future blog has a post from 22 January 2008 about negative reaction to 23andMe.
I learned from GenomeWeb today that on 8 February 2008, Helicos BioSciences announced that it had sold its first sequencer. Yesterday, Expression Analysis confirmed that they were the purchaser. Expression Analysis said they will use the sequencer for “de novo sequencing, candidate gene sequencing, and digital gene expression.”
March 04 2008 | Biology | Comments Off
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