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Tuesday, January 19, 2016

All about Craig

The sequence of the human genome was announced on June 26, 2000 although the actual sequence wasn't published until a year later. There were two sequences. One was the product of the International Human Genome Project led by Francis Collins who said,
"It is humbling for me and awe-inspiring to realize that we have caught the first glimpse of our own instruction book, previously known only to God."
The sequence was a composite of a number of individuals.

The second sequence was from Celera Genomics, led by Craig Venter. It was mostly his genome, making him the second being to know his own instruction book ... right after God.

It took another seven years to finish and publish the complete sequence of all of Craig Venter's chromosomes. The paper was published in PLoS Biology (Levy et al., 2007) and highlighted in a Nature News article: All about Craig: the first 'full' genome sequence.

What's unique about this genome sequence—other than the fact that it's God's Craig Venter's—is that all 46 chromosomes were sequenced. In other words, enough data was generated to put together separate sequences of each pair of chromosomes. That produces some interesting data.

There were 4.1 million differences between homologous chromosomes (22 autosomes). 78% of these events were single nucleotide polymorphisms (SNPs). The rest were indels (insertions and deletions) and these accounted for 0.9 million nucleotides. Thus, indels made up 74% of the total number of variant nucleotide sequence.

In addition, there were 62 copy number variants (duplication) accounting for an additional 10Mb of variation between haploid sets of chromosomes. The total number of nucleotide differences is 13.9Mb when you add up all the indels, SNPs, and duplications. The two haploid genomes differ by about 0.5% by this calculation (total amount sequenced was 2,895Mb).

When the two copies of all annotated genes were compared, it turned out that 44% were heterozygous—the two copies were not identical.

Craig Venter's genome sequence differs from the composite human reference genome at 4,118,889 positions. Most of these were already known as variants in the human population but 31% were new variants (in 2007).

Venter has written about his genome sequence in A Life Decoded. He has variants in his APOE gene sequence that are associated with Alzheimer's and cardiovascular diseases. He has variants in his SORL1 that also make him at risk for Alzheimer's according to 2007 data. Just about everyone who gets their genomes sequenced will find variants that put them at greater risk for some genetic disease.

Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., Axelrod, N., Huang, J., Kirkness, E.F., Denisov, G., Lin, Y., MacDonald, J.R., Pang, A.W.C., Shago, M., Stockwell, T.B., Tsiamouri, A., Bafna, V., Bansal, V., Kravitz, S.A., Busam, D.A., Beeson, K.Y., McIntosh, T.C., Remington, K.A., Abril, J.F., Gill, J., Borman, J., Rogers, Y.-H., Frazier, M.E., Scherer, S.W., Strausberg, R.L., and Venter, J.C. (2007) The diploid genome sequence of an individual human. PLoS Biol, 5(10), e254. [doi: 10.1371/journal.pbio.0050254]


Aceofspades said...

He has also been known (allegedly) for throwing bones to creationists when it comes to junk DNA.

EN&V have been happy to claim him as an ally in the junk DNA wars although I cannot find an original source on this so i can't confirm or deny whether he actually said certain things.

Mikkel Rumraket Rasmussen said...

A while ago there was a big fuss about Venter allegedly denying universal common descent in a public panel with Richard Dawkins and a couple of other famous scientists. IIRC Dawkins asked Venter whether a universal genetic code implied common descent, to which Venter actually didn't really reply but just chuckled a bit and looked at Dawkins in a strange way. This was interpreted by all the worlds creationist lunatics to mean Craig is denying common descent. What he really meant by his response is anyone's guess.

See this youtube video: Dr. Craig Venter Denies Common Descent in front of Richard Dawkins!

Mikkel Rumraket Rasmussen said...

Ahh Francis Collins. The man who's reasons for belief in god was that he had a difficult time dealing with dying cancer patients and once saw a frozen waterfall when out jogging - Therefore a virgin gave birth to a man who resurrected himself in a sacrifice to himself and that man is god.

Joe Felsenstein said...

Whatever one thinks of Craig Venter, the fact that the sequence is of one individual is not as important as seems. Every generation our genomes get reassembled from parts of our parents' sequences. If you take the 46 chromosomes and sequence each one from a different individual in a population, you get a possible individual from that population. Venter's sequence is unusual in having resolved the haplotypes in all parts of the genome. But the fact that they came from the same individual will not give us as much new information as one might think.

Larry Moran said...

The information may not be Earth-shattering but it's useful to see a "complete" genome sequence. It tells us a bit about variation and it emphasizes the fact that heterogeneity is important. People who get their "genome" sequenced need to understand this point.

I'd love to know if Venter's chromosomes (from whatever tissue was tested) are exactly the same as his parents' (except for a few mutations). In other words, how important is somatic cell recombination and rearrangement?

Larry Moran said...

We know exactly what Craig Venter meant. He meant that there is no universal tree of life because it's been obscured by horizontal gene transfer.

The only amazing thing about that video is the fact that Richard Dawkins didn't know this.

Petrushka said...

Didn't Venter assemble a genome from scratch? Therefore ID?

Aceofspades said...

Yes I remember that too and I agree with Larry... he was misunderstood.

But according to evolution news and views, at a talk at the Seattle town hall in 2013 he made the following statements:

> " DNA is "software" that contains "digital information" or "digital code."

> "Life is a DNA software system,"

> People have "arrogantly called parts of the human genome that don't code for protein 'junk DNA.'". Today junk DNA is "where all the discoveries are happening" and we know that junk DNA is crucial for gene regulation

> we "only have minimal understanding" of how junk DNA works, and so we have a lot to discover in that area.

> he said said he knows people whose junk DNA he'd like to remove but doesn't recommend doing it

I don't know to what extent they have misrepresented him.

Faizal Ali said...

The only source for that post is Casey Luskin's recollection of a lecture he attended. I need not elaborate on why that may not be the most reliable, do I?

Aceofspades said...
This comment has been removed by the author.
Aceofspades said...

That's why I said: "I don't know to what extent they have misrepresented him." and "I cannot find an original source on this so I can't confirm or deny whether he actually said certain things".

Having said that I wouldn't be surprised if he had said things similar to this because I hear nonsense like this from geneticists all the time.

Jmac said...

" "It is humbling for me and awe-inspiring to realize that we have caught the first glimpse of our own instruction book, previously known only to God."

I didn't even know that Craig Venter believed in God. He must be one of those many atheists who changed their mind after they really realized how complex and beautiful the human genome is; Anthony Flew just being one of them.

Jmac said...

"We know exactly what Craig Venter meant. He meant that there is no universal tree of life because it's been obscured by horizontal gene transfer."

Really? Why would Venter say then"...I don't think there is only one form of life on this planet"? If there are more than one form of life on this planet, how could they descent from each other?

I'm always amazed how evolutionist can read others minds; what they mean and what they were actually trying to say. It must be an evolutionary miracle...

Larry Moran said...


Read my blog: Craig Venter Discusses the Tree of Life.

Listen to the video, beginning at the 9 min mark. Try and listen carefully. Try and understand what Craig Venter meant when he said there were different life forms on this planet.

BTW, Craig Venter is an atheist. You really, really, need to learn how to read for comprehension.

AllanMiller said...

@Larry We know exactly what Craig Venter meant. He meant that there is no universal tree of life because it's been obscured by horizontal gene transfer.

The only amazing thing about that video is the fact that Richard Dawkins didn't know this.

Dawkins was specifically intrigued by Venter's claim that the different genetic codes may mean different deep origins. "The DNA code of all creatures that have ever been looked at is all but identical. Surely that means that they are all related ... doesn't it?". Whether the genetic code in LUCA had its origins in prior HGT or not, common descent from that LUCA appears to be well supported by the virtual invariance of the code. HGT into multiple lineages is less plausible than vertical descent and divergence, at least.

Jmac said...

Reading with comprehension? How do you explain Venter's quote:
"It is humbling for me and awe-inspiring to realize that we have caught the first glimpse of our own instruction book, previously known only to God."

Craig Venter surely doesn't sound like an atheists to me who believes that random processes "created" the genetic code.

Maybe you can enlighten me and the rest what Craig Venter meant when he wrote those humbling words, because I have only one explanation for such words.

Faizal Ali said...

Craig Venter never said that:

Oh dear. How embarrassing and humiliating this must be for you, Eric. It took me exactly 0.53 seconds to find that on Google. Too much work for you, I guess.

Jmac said...


I totally disagree that Venter believes in common descent while he only admits it indirectly, he is aware of the consequences of it and the bulling that will follow if he did. His funding would suffer too and the investors would not be happy...

When one carefully follows the discussion from the beginning of the video Larry linked us to, it is clear that the thread of the conversation was “what life is?” and how to define it.

Chris Mackay from NASA suggested that finding another form of life elsewhere would help defining what really life is if it can be compered to another form of life.

However, Venter disagrees that there is only ONE FORM OF LIFE ON EARTH ALREADY by questioning the universality of the genetic code, the variety of metabolisms, variety of organisms in response to Paul Davis’ claim that “…we all have a common ancestor, we have the same genetic code…”

This is at the 9 minute mark but watch the whole video without bias. Christ Mackays comment at 5:45 made my day. It probably spoiled the day of evolutionists with an open mind but how many of them are out there?

Mikkel Rumraket Rasmussen said...

Eric is confusing Francis Collins with Craig Venter. Eric, they're two different persons. This is implied foremost by the fact that their names are different.

With that out the way, I also have to agree I don't think Craig was being very clear about what he meant. Though I wouldn't swing the creationist way and believe he denies common descent, since I simply don't know what he believes, he's not made it clear anywhere that I'm aware of.

The whole discussion was rather vague and muddled and key words were not really defined well. For example, what do any of them mean by another "form" of life?

In the context of what they were discussing: the possibility and properties (and our ability to detect) extraterrestrial life, it makes little sense for Venter to start blathering about Bushes vs Trees, different metabolic cycles, deep divergences and sligthtly altered codes in endosymbiotic plastids.

Add to this that in response to a direct question from Dawkins, he doesn't actually answer it. One can be excused for not being convinced that anyone "knows exactly what Craig Venter meant". I don't.

Whether Dawkins is aware that the root is bush-like is totally immaterial with respect to the question being asked, which is whether a shared and "all but identical" genetic code implies common descent or not. Nothing you've said, Larry, makes it any more clear what Craig believes.

Why creationists take consolation in any of this is beyond me however, we are talking about divergences over 3 billion years old. Yet the shared descent that matters most to creationists is Homo Sapiens vs Everything else. I'll gladly take a bet on whether Craig Venter believes humans are primates, mammals, vertebrates, chordates, metazoa and eukaryotes too.

Whether Single-celled prokaryote A shares an ancestor with Single-celled prokaryote B some threethousand fivehundred million years ago doesn't sound to me like a theologically important question. Yes this is the kind of "common descent" creationists think Craig Venter is denying. Why the fuck would that even matter?

SRM said...

Yes this is the kind of "common descent" creationists think Craig Venter is denying. Why the fuck would that even matter?

Good summary of the situation, I think. But as to your question, it matters to the creationist given their mindset. Often their goals aren’t to promote their ridiculous ideas directly (this is why they criticize scientific ideas while remaining rather vague about their own alternatives), but rather to generally discredit the scientific way of knowing, as a means to an end.

These are the people who will criticize science/scientists for being arrogant in their certainty of knowing everything and lacking humility. But when it is pointed out that the whole point of the scientific method is to investigate the unknown and that all accrued knowledge is by definition provisional, they will spin on a dime and criticize science for not being able to figure out everything with certainty and say it must therefore be a flawed pathway to knowledge (unlike faith in revelation).

So in their mindset, any new idea and any uncertainty regarding old ideas is a flaw they can use to promote their anti-science perspective. This is a general long-term goal they hope will bleed forth to a time when we can all go back to believing that the earth is under heaven, that it was created 6000 years ago, and that their (almost always Christian) god sparked all life into existence by some sort of undefined magic.