In 1944, a Columbia University doctoral student in genetics named Evelyn Witkin made a fortuitous mistake. During her first experiment in a laboratory at Cold Spring Harbor, in New York, she accidentally irradiated millions of E. coli with a lethal dose of ultraviolet light. When she returned the following day to check on the samples, they were all dead except for one, in which four bacterial cells had survived and continued to grow. Somehow, those cells were resistant to UV radiation. To Witkin, it seemed like a remarkably lucky coincidence that any cells in the culture had emerged with precisely the mutation they needed to survive so much so that she questioned whether it was a coincidence at all.
For the next two decades, Witkin sought to understand how and why these mutants had emerged. Her research led her to what is now known as the SOS response, a DNA repair mechanism that bacteria employ when their genomes are damaged, during which dozens of genes become active and the rate of mutation goes up. Those extra mutations are more often detrimental than beneficial, but they enable adaptations, such as the development of resistance to UV or antibiotics.
The question that has tormented some evolutionary biologists ever since is whether nature favored this arrangement. Is the upsurge in mutations merely a secondary consequence of a repair process inherently prone to error? Or, as some researchers claim, is the increase in the mutation rate itself an evolved adaptation, one that helps bacteria evolve advantageous traits more quickly in stressful environments?
The scientific challenge has not just been to demonstrate convincingly that harsh environments cause nonrandom mutations. It has also been to find a plausible mechanism consistent with the rest of molecular biology that could make lucky mutations more likely. Waves of studies in bacteria and more complex organisms have sought those answers for decades.
The latest and perhaps best answer for explaining some kinds of mutations, anyway has emerged from studies of yeast, as reported in June in PLOS Biology. A team led by Jonathan Houseley, a specialist in molecular biology and genetics at the Babraham Institute in Cambridge, proposed a mechanism that drives more mutation specifically in regions of the yeast genome where it could be most adaptive.
Its a totally new way that the environment can have an impact on the genome to allow adaptation in response to need. It is one of the most directed processes weve seen yet, said Philip Hastings, professor of molecular and human genetics at Baylor College of Medicine, who was not involved in the Houseley groups experiments. Other scientists contacted for this story also praised the work, though most cautioned that much about the controversial idea was still speculative and needed more support.
Rather than asking very broad questions like are mutations always random? I wanted to take a more mechanistic approach, Houseley said. He and his colleagues directed their attention to a specific kind of mutation called copy number variation. DNA often contains multiple copies of extended sequences of base pairs or even whole genes. The exact number can vary among individuals because, when cells are duplicating their DNA before cell division, certain mistakes can insert or delete copies of gene sequences. In humans, for instance, 5 to 10 percent of the genome shows copy number variation from person to person and some of these variations have been linked to cancer, diabetes, autism and a host of genetic disorders. Houseley suspected that in at least some cases, this variation in the number of gene copies might be a response to stresses or hazards in the environment.
In 2015, Houseley and his colleagues described a mechanism by which yeast cells seemed to be driving extra copy number variation in genes associated with ribosomes, the parts of a cell that synthesize proteins. However, they did not prove that this increase was a purposefully adaptive response to a change or constraint in the cellular environment. Nevertheless, to them it seemed that the yeast was making more copies of the ribosomal genes when nutrients were abundant and the demand for making protein might be higher.
Houseley therefore decided to test whether similar mechanisms might act on genes more directly activated by hazardous changes in the environment. In their 2017 paper, he and his team focused on CUP1, a gene that helps yeast resist the toxic effects of environmental copper. They found that when yeast was exposed to copper, the variation in the number of copies of CUP1 in the cells increased. On average, most cells had fewer copies of the gene, but the yeast cells that gained more copies about 10 percent of the total population became more resistant to copper and flourished. The small number of cells that did the right thing, Houseley said, were at such an advantage that they were able to outcompete everything else.
But that change did not in itself mean much: If the environmental copper was causing mutations, then the change in CUP1 copy number variation might have been no more than a meaningless consequence of the higher mutation rate. To rule out that possibility, the researchers cleverly re-engineered the CUP1 gene so that it would respond to a harmless, nonmutagenic sugar, galactose, instead of copper. When these altered yeast cells were exposed to galactose, the variation in their number of copies of the gene changed, too.
The cells seemed to be directing greater variation to the exact place in their genome where it would be useful. After more work, the researchers identified elements of the biological mechanism behind this phenomenon. It was already known that when cells replicatetheir DNA, the replication mechanism sometimes stalls. Usually the mechanism can restart and pick up where it left off. When it cant, the cell can go back to the beginning of the replication process, but in doing so, it sometimes accidentally deletes a gene sequence or makes extra copies of it. That is what causes normal copy number variation. But Houseley and his team made the case that a combination of factors makes these copying errors especially likely to hit genes that are actively responding to environmental stresses, which means that they are more likely to show copy number variation.
The key point is that these effects center on genes responding to the environment, and that they could give natural selection extra opportunities to fine-tune which levels of gene expression might be optimal against certain challenges. The results seem to present experimental evidence that a challenging environment could galvanize cells into controlling those genetic changes that would best improve their fitness. They may also seem reminiscent of the outmoded, pre-Darwinian ideas of the French naturalist Jean-Baptiste Lamarck, who believed that organisms evolved by passing their environmentally acquired characteristics along to their offspring. Houseley maintains, however, that this similarity is only superficial.
What we have defined is a mechanism that has arisen entirely through Darwinian selection of random mutations to give a process that stimulates nonrandom mutations at useful sites, Houseley said. It is not Lamarckian adaptation. It just achieves some of the same ends without the problems involved with Lamarckian adaptation.
Ever since 1943, when the microbiologist Salvador Luria and the biophysicist Max Delbrck showed with Nobel prize-winning experiments that mutations in E. coli occur randomly, observations like the bacterial SOS response have made some biologists wonder whether there might be important loopholes to that rule. For example, in a controversial paper published in Nature in 1988, John Cairns of Harvard and his team found that when they placed bacteria that could not digest the milk sugar lactose in an environment where that sugar was the sole food source, the cells soonevolved the ability to convert the lactose into energy. Cairns argued that this result showed that cells had mechanisms to make certain mutations preferentially when they would be beneficial.
The rest is here:
Beating the Odds for Lucky Mutations - Quanta Magazine
- June 11th At Westport, CT: Federal Red Flags, HIPAA Security Rules and Fraud Prevention - November 7th, 2009 [November 7th, 2009]
- Do not learn Dvorak! - November 7th, 2009 [November 7th, 2009]
- You Can’t Solve Problems By Making It Illegal To Have The Problem - November 7th, 2009 [November 7th, 2009]
- A Force Fix for Healthcare - November 7th, 2009 [November 7th, 2009]
- Yahble, HIT, Bubblecon, BIZDEV!, Solid State - November 7th, 2009 [November 7th, 2009]
- 15 things that suck about the Palm Pre - November 7th, 2009 [November 7th, 2009]
- What an Indie Genomics Lab Looks Like - November 7th, 2009 [November 7th, 2009]
- Practice Fusion: Class D Felony? - February 26th, 2010 [February 26th, 2010]
- Practice Fusion Responds - March 7th, 2010 [March 7th, 2010]
- Practice Fusion: Do the math: $44,000 is a LIE - March 10th, 2010 [March 10th, 2010]
- How Much Until Doctors Approve of 23andMe? - March 10th, 2010 [March 10th, 2010]
- Biochemicals as Media, Not Methods - March 10th, 2010 [March 10th, 2010]
- More Practice Fusion Reality Distortion - March 10th, 2010 [March 10th, 2010]
- Same Test Results: 23andMe is Myriad is BRCA is Medicine - March 12th, 2010 [March 12th, 2010]
- BRCA is 23andMe is Myriad is Medicine - March 13th, 2010 [March 13th, 2010]
- Getting Serious About Genomics as Common Medical Practice - March 15th, 2010 [March 15th, 2010]
- The New John Mackey of Genetics: Linda Avey? - March 15th, 2010 [March 15th, 2010]
- Keep the Medical, Well, Medical - March 16th, 2010 [March 16th, 2010]
- If 23andMe shuts down, it won’t be for some mundane reason like the bills weren’t paid - March 16th, 2010 [March 16th, 2010]
- If I Run A Medical Practice, How Do I Use A 23andMe? - March 17th, 2010 [March 17th, 2010]
- 23andMe Contract in Bad Faith - March 19th, 2010 [March 19th, 2010]
- Doctors CANNOT Use 23andMe Due To 23andMe’s Bad Faith Contract - March 20th, 2010 [March 20th, 2010]
- Pathway Compared to 23andMe and Navigenics - March 22nd, 2010 [March 22nd, 2010]
- There’s a Word for “Views Differ” When One View Is The State - March 24th, 2010 [March 24th, 2010]
- Association for Molecular Pathology, et al. v. USPTO, et al. – Opinion - March 29th, 2010 [March 29th, 2010]
- Birth of a Super Villain - April 3rd, 2010 [April 3rd, 2010]
- “Medical Products” like 23andMe must not become the new “Financial Products” - April 4th, 2010 [April 4th, 2010]
- How I Would Apply Genomic Technology In Clinical Use Today - April 5th, 2010 [April 5th, 2010]
- Gmail Enterprise: World’s Best EMR - April 6th, 2010 [April 6th, 2010]
- Brief Primer on Health Law Compliance - April 9th, 2010 [April 9th, 2010]
- Spoiler: You ARE the “Valids” - April 9th, 2010 [April 9th, 2010]
- Rachel Lehmann-Haupt Line by Line Take Down - April 9th, 2010 [April 9th, 2010]
- Is Medicare Bankrupt? What the Hell Is Going On? - April 17th, 2010 [April 17th, 2010]
- The Big Shuffle: Medicare Cuts Rates by 21.3% (but not “technically”) - April 17th, 2010 [April 17th, 2010]
- “Tech Hiring Binge” == “Fear for Your Job, Nerds” - April 18th, 2010 [April 18th, 2010]
- How Bad is Bad? $.20 on the Private Medical Insurance Dollar - April 20th, 2010 [April 20th, 2010]
- Update: How Bad is Bad? It Used to Be $.45 on the Medical Insurance Dollar - April 20th, 2010 [April 20th, 2010]
- World’s Best “EMR” for $1000: Google Spreadsheets + iPad - April 21st, 2010 [April 21st, 2010]
- Don’t Insult Me with your “AOL Keyword” Strategy, Google Health - April 21st, 2010 [April 21st, 2010]
- How to Play LAWGAMES - April 23rd, 2010 [April 23rd, 2010]
- Top 4 Predatory Schemes Encroaching on American Medicine: Part 1 - April 25th, 2010 [April 25th, 2010]
- What’s the Big Deal About iPads? - April 27th, 2010 [April 27th, 2010]
- Got Google Android for Google I/O - April 27th, 2010 [April 27th, 2010]
- Google Enterprise meets HIPAA and HITECH Compliant Laws - April 29th, 2010 [April 29th, 2010]
- Pixels of Accuracy CHALENGE: Diagnostic Medical Imaging - April 29th, 2010 [April 29th, 2010]
- 23andMe Launder AlioGenetics Doesn’t Even Bother to Remove 23andMe Logo - April 30th, 2010 [April 30th, 2010]
- Anthem of CT Denies $600 Until “Subscriber Responds to our Coordination of Benefits Questionnaire” - May 1st, 2010 [May 1st, 2010]
- Apple And Google Team Up To Launch Revolutionary Mobile Health System - May 1st, 2010 [May 1st, 2010]
- Funny Pictures from This Year Building the Medical Practice - May 6th, 2010 [May 6th, 2010]
- Remote Medical Video Monitoring on iPad and iPhone - May 7th, 2010 [May 7th, 2010]
- Google Calendar Overhead Waiting Room Display - May 7th, 2010 [May 7th, 2010]
- Various Whiteboards on Solid State Medical Operations - May 7th, 2010 [May 7th, 2010]
- The Raw Facts about Counsyl - May 7th, 2010 [May 7th, 2010]
- Brawndo: Still Mutilating Thirst, Still Not Yet Sold at the Stop-n-Shop Pharmacy - May 9th, 2010 [May 9th, 2010]
- Video: Google Enterprise to Outsource Medical Administration - May 9th, 2010 [May 9th, 2010]
- Gattaca: “The Matrix” of Genomics - May 11th, 2010 [May 11th, 2010]
- 23andMe Now Diagnoses Fatal Tay-Sachs Disease - May 12th, 2010 [May 12th, 2010]
- Why Was Pathway Targeted for FDA Enforcement and Not 23andMe? - May 15th, 2010 [May 15th, 2010]
- John Dolan on Aging and the Horrifying Conclusion of GWAS - May 16th, 2010 [May 16th, 2010]
- Sam R. Riley Wants To Tell You About Practice Fusion - May 17th, 2010 [May 17th, 2010]
- Response to “Genomic Medicine: Lost” - May 19th, 2010 [May 19th, 2010]
- Death And Taxes: CMS to IRS - May 19th, 2010 [May 19th, 2010]
- Please Stop Antagonizing the AMA - May 26th, 2010 [May 26th, 2010]
- Dan Vorhaus, Attorney At Law, Legally Advises Medical Doctors Can Use 23andMe To Provide Medical Advice - May 28th, 2010 [May 28th, 2010]
- Singularity Summit 2010 in San Francisco to Explore Intelligence Augmentation - June 7th, 2010 [June 7th, 2010]
- OpenPCR: DNA amplification for anyone - June 10th, 2010 [June 10th, 2010]
- FDA sends letters to 5 genetic testing companies - June 11th, 2010 [June 11th, 2010]
- Amazon And The NIH Team Up To Put Human Genome In The Cloud - March 31st, 2012 [March 31st, 2012]
- ReproSource Comments on New Study Linking Infertility to Genetics - April 25th, 2012 [April 25th, 2012]
- Genetics 101 Part 1: What are genes? - Video - April 30th, 2012 [April 30th, 2012]
- Red Ice Radio - David Icke - Hour 1 - The Manipulation of Humanity - Video - April 30th, 2012 [April 30th, 2012]
- Genetics Part 5: Human Genetic Disorders - Video - April 30th, 2012 [April 30th, 2012]
- C2CAM - The Nephilim, Genetic Manipulation - April 30th, 2012 [April 30th, 2012]
- Human Nature talk with Robert Sapolsky, Gabor Mate, James Gilligan, Richard Wilkinson - Video - April 30th, 2012 [April 30th, 2012]
- Human Genetic Diseases - Video - April 30th, 2012 [April 30th, 2012]
- Alien Scientist on Genetics, Implants - April 30th, 2012 [April 30th, 2012]
- Research and Markets: Genetics, 6th Edition International Student Version Continues To Educate Today's Students for ... - May 4th, 2012 [May 4th, 2012]
- Myriad Genetics to Present at the Bank of America Merrill Lynch 2012 Health Care Conference - May 4th, 2012 [May 4th, 2012]
- Genetics may explain some people's dislike of meat - May 4th, 2012 [May 4th, 2012]
- 'Blond Genes' May Vary Around the World - May 4th, 2012 [May 4th, 2012]