I’m on my way to this symposium, “Humanity’s Genes and the Human Condition,” at UC Berkeley. It should be a day of interesting and relevant talks, especially since the American Society of Human Genetics had their annual meeting this week, and lots of discussions were held about genetic ancestry testing. I’m looking forward to hearing Svante Pääbo and Karin Stromswold talk about human evolution and language, respectively.
If I can live blog, you should check out this post regularly to see minute by minute updates. If I can’t live blog, I will be taking notes the old fashioned way and updating this post later on with my thoughts.
9:04 am: Everyone is getting settled, seems like it’ll be a lively conference. I am live blogging on my phone so excuse the typos.
9:07 am: Joe Palca of NPR is introducing the program. He’s the moderator.
9:10 am: Ed Penhoet is talking about the intersection of genomics and the social sciences. Nobel Prize lecture Sydney Brenner and Gordon Moore (both are in the crowd!) are acknowledged, and the last issue of Science and the genetics of behavior.
9:21 am: David Botstein is taking the stage for the keynote speech. Admits he has no idea what this conference is all about. Everyone laughs.
9:25 am: Botstein is defining many terms like structural & functional genomics. Slide up on size of genomes. Function has little to do with number of genes. Structure and function of protein encoded genes are conserved. He calls it the breadcrumbs of evolution, I like the analogy.
9:32 am: Sequence comparison of DNA is a function of time and the basis of comparing genomes. Tricky inference with associating a gene to a function. The sequence means nothing to function, until it changes the function of the protein. He’s now talking about reviving knockout yeast with inserted human equivalent genes.
9:37 am: Introduced multiple sequence alignments and drawing phylograms. Defining orthologs and paralogs, seems like an intro to genetics 101 class. Talking about duplications in tumorigenesis and using yeasts to see how tumor genes from colon cancer affect yeast phenotyping. Finding mutant genes in humans and using yeast homologs to seek out functional effects.
9:43 am: Variations in sequences, fragment length, one if the first methods to determine how genes vary from one person to another. Distinguishing individuals, DNA hype in pop culture. Using DNA variation in CSI, CODIS: the 13 markets that define the individual.
9:47 am: Single gene diseases like Huntington’s and cystic fibrosis can tell us about basic biological functions of the genes.
9:49 am: Mapping the genome with a microarray chip the has a representative of every gene. Can learn expression of genes in certain tissues at certain developmental stages. Gene expression at certain tissues and stages are conserved between individuals.
David Botstein, Joe Palca, Jasper Rine
9:54 am: Everyone needs a basic understanding of statistics and probabilities. Q&A session with Jasper Rine and Joe Palca.
Jasper Rine took a snipe at ancestry testing, “cheaper assays at determining blue eyes and ear wax.” Haha.
10:37 am: Coffee break is over. Svante Pääbo is taking the stage. Thanking Sydney and confused on howto pitch his talk. Seems like the organizers didn’t prep speakers enough.
Using sequence comparison to understand human evolution. Nothing particularly new being said, but he’s estimating the most common recent ancestor of human-chimp at 4-5 million years ago.
How much variation in human populations exist? 4 base pair differences in 100,000 bases per individual. Shows a tree of gorillas to chimps to bonobos to orangutans and humans.
10:45 am: Are there common variations in populations in Asia, Africa and Europe? There is some geographic-genetic structure to populations. Focus on variants, there are specific variants to each major continent.
10:48 am: Stressing what happened to human lineage after the split from the most common recent ancestor with chimps. Our first problem is defining how humans are unique. We have had a hard time defining human nature: language and tool use in nonhuman primates.
10:50 am: Did human nature evolve recently? We must use Neandertals to find that out but the technical challenge is that Neandertals are thought to be extinct. Replacement vs. Integration of the two species.
10:52 am: High-throughput sequencing let’s us figure out the above questions. Shoutout to 454 technologies, says well have 3 billion base pairs of Neandertal genome by the end of this year. Contamination and degradation of aDNA discussion.
10:55 am: Only .5% contamination has been identified by the last sequencing freeze. Last common ancestor to Neandertals is 800,000 years ago. Neandertals ate deeply diverged. Did mixing occur? Replacement and assimilation again.
10:57 am: Does a random European or African look like a Neandertal genetically? Not right now, but we will have more data. He’s conservative, ‘not by much.’ Loci on chromosome 17, fertility gene western Europe and Eurasia, do modern humans share this sequences? No, but we need to look at more Neandertals.
11:01 am: He’s sequencing Neandertals not for Neandertals but for a greater understanding of what makes us humans. Now talking about drift and selective swifts, looking for positive selection on modern humans.
Dan Rokhsar, a discussant, is taking the stage. Discussion variation within humans, why did Neandertals die out? Division of labor? Language? Tool making? Agriculture?
11:10 am: Quoting Kremer: more people more brilliant minds, population bottleneck type talk. Humans took advantage of population boom. Question about language, FOXP2, no reason to think Neandertals didnt have language, but talked about recent selective sweep in modern human. Question about what does the 1.2% difference between human & chimp genomes and one about alignments of genomes of modern populations.
11:18 am: Tim White on stage. Talks about religious opposition to human evolution and shows us lots if human fossils. The fossils tell us what they looked like, what they ate, what tools they used. Recommends a synthesis of DNA and fossil evidence.
11:21 am: Tim talks about Prabhakar’s paper on finding the unique allele that makes human opposable thumbs. Points out exhibit on human evolution, encourages inspiring youngins.
11:24 am: Question about unique genes to agriculture. Lactose tolerance, audience points out. Amylase and sickle cell. Surprised that Paabo didn’t answer this. An audience member had to answer it! Anyways, culture in these situations led to genetic changes. Question about Flores hominid genomics. Svante says he tried a tooth but did not work. Tim is asked to comment on controversy between paleontology and genetics, about human-chimp split. Paleontologists were wrong in thinking humans-chimps split 15 mya because they interpretted the fossil record incorrectly. Suggests a spring date for Ardipithecus publication that could be most common ancestor. Question about why Neandertals died? Svante says Tim is the paleontologist, Tim bounces back saying Svante is the European!
11:31 am: Moving to talk about infectious diseases. I’m taking a live blogging silence to conserve battery power because after lunch there will be a talk about language. I’ll update this with my old fashioned notes later at home.
Svante Paado & Tim White
1:45 pm: I’m back from lunch. The last talk on immunology was fascinating and I’ll fill in the hand written notes later. Now, Karin Stromswold is gonna talk about language.
1:51 pm: She’s defining language and linguistics and how language touches so many fields like neuroscience, genetics, clinical sciences, pyschology. She’s going to talk about what we know and don’t know about language.
11:54 pm: People do differ in linguistic abilities. Two year old have different know number of words and fluency/proficiency of second languages. What about language impairment, not hearing, so do genetic factors play a role in linguistic variability. She’s drawing an analogy of the genetics if language to the genetics of finger length and number of fingers. Different variants can knock out language while others can effect the extent of language cognition.
1:59 pm: 9+ loci linked to dyslexia and language disorder. She’s talking about the KE family, automsomal disorder. She’s bringing up the new FOXP2-CNTNAP2 paper and how downstream targets of FOXP2 also affect language phenotypes.
2:02 pm: Language disorders do cluster in families despite the fact there’s not a clear Mendelian inheritance. She’s bringing up twin studies to quantify the extent language is genetic. Probability of language impairment between more-or-less identical twins. Compared many variables, between language related and non-language. Vocab is least genetically related, but syntax is.
2:07 pm: Overlap of linguistic and non- linguistic, genetic correlation between fine motor division and linguistic abilities. Why is there a great overlap between syntax and articulation? Perceptive vs. Production. Maybe there’s a hierarchical structure? Not the linear order!
2:11 pm: Key feature of language is that we can embed sentences within each other. Language apes can’t! Argued that us the only specific feature of human communication. We can see non human organism model, but can’t embed multiple messages.
2:13 pm: Genetics affects all aspects of language, and some are specific. Specific neural circuitry, ie articulation and syntax. Different evolutionary histories for faculty. She’s rushing because she’s out if time. Summarizing pleiotropy and phenotype manifests different at different ages. Child can’t speak at two but recovers 100% later, but develops slower.
2:19 pm: Common alleles that contribute to a disease under a environment may not in a different environment. The whole genome + environment = phenotype.
2:20 pm: Dan Geschwind and Marc Feldman take the stage.
Joe Palca, Dan Geschwind and Marc Feldman
Dan’s talking about specificity, genes of language are related to other cognitive traits. He’s talking about CNTNAP2 and where it is expressed and regulated, and assigning function. Asks about recursion, does it have specific heritabilty? Are frontal systems for memory and planning that help us with lanuage? Language us built on existing systems. “We have assymetric brains while chimps don’t,” that’s what Dan says. Karin is explaining how a combination if traits is more complex than keeping things in memory.
2:28 pm: Marc explains the problems of the language if genetics. Herditabilty of height is 90%, know 30 SNPs, but the height of Japanese changed 4 inches in a couple generations. No major genetic changes in the Japanese. Warns that we must be careful with heritability because it doesn’t indicate penetrance. Mentions the New York Times recent coverage on genetics and epigenetic phenomenon.
2:33 pm: Marc says language and genetic trees of populations are very similar, almost too similar. Language and genes are almost synonymous. History of humans is if migrations and who married whom. People marry others who speak their language more often than not, so that’s why languages and genetics correlate.
2:36 pm: “Heritabilities account for the amount of variation,” Karin. Marc says that 30% heritability isn’t good enough. 60% variance due to environment is too random. Audience questions recursion in starlings, which refutes humans being only recursive communicators. Karin, “starlings aren’t technically recursive.” There’s a bit of a pissing match between the two, it gets heated. Joe Palca had to moderate. Molecular biologist asks for definition of recursive.
2:42 pm: Genetics of psychosis up next. I’m gonna stop live blogging again to save battery power. I thought my battery would last longer. I’ll update my hand written notes later.
4:53 pm: Sydney Brenner is about to come up. He’s gonna tell us if this was a successful talk.
4:54 pm: Starts off with a zinger: “Biological evolution for humans has stopped.” Uhh, really Sydney? You better do better than that. He uses an analogy about how if we feel cold, we don’t ‘adapt’ we just kill an animal, skin it, and wear its pelt as evidence of relaxed natural selection. I can see how he’s gonna use cultural evolution as a foundation for the rest of his wrap up, but he didn’t use a good analogy!
4:58 pm: Sydney Brenner coins a new term, social therapeutics. Calls it the new public health. The most outstanding and impacting breakthrough of public health in the last two centuries was advising the public to keep drinking, potable water separate from soiled water. Asks what is the new challenge for public health for the 21st century?
5:00 pm: Obesity! Lists how our hypothalamus drives us to eat more and convert to fat which means our genomes are mal-adapted to the current cultural environment. Jokes that obesity should be a crime. He points out Alta Charo, the previous speaker on Ethics & Epigenetics. Says she must be jailed and forced to cycle to generate electricity. Sydney advocates that this will kill two birds with one stone, obesity and the energy crisis. There are some uncomfortable laughs. The joke isn’t being taken that well.
5:05 pm: Moves on to say that science is extremely flawed nowadays. In his hay day, science was medieval. There was a skilled journeyman and a cohort of apprentices that sought to learn and absorb their mentor’s knowledge. Nowadays big science, big pharmaceuticals and what not, has created drones. Lost is the creative thinking process. The public depends on big science to solve problems, pill for this pill for that, pill for something else. Says, “We must be accountable for our own health.”
5:11 pm: Further advocates to study our fellow humans. How did the human eye evolve? Why not use blind people to see what certain allelic variants cause different phenotypes. We don’t need elaborate mouse models, the world is one big petri dish and the whole human population is one big experiment.