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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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July 29, 2010

Craig Venter, Venting

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Posted by Derek

Craig Venter has never been a person to keep a lot of things bottled up inside him. But check out this interview with Der Speigel for even more candor than usual. For instance:

SPIEGEL: Some scientist don't rule out a belief in God. Francis Collins, for example …

Venter: … That's his issue to reconcile, not mine. For me, it's either faith or science - you can't have both.

SPIEGEL: So you don't consider Collins to be a true scientist?

Venter: Let's just say he's a government administrator.

There's more where that came from. The title is "We Have Learned Nothing From the Genome", and it just goes right on from there. Well worth a look.

Comments (78) + TrackBacks (0) | Category: Biological News


COMMENTS

1. Handles on July 29, 2010 10:16 PM writes...

"But we don't need any more Neanderthals on the planet, right? We already have enough of them."

Seems like he could really liven up a dinner party after a few glasses of wine. Great interview.

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2. Nat on July 29, 2010 10:40 PM writes...

Ugh. I think Craig Venter is one of the greatest scientists of our era, but this interview is a good reminder of exactly why everyone thought he was a self-aggrandizing jerk ten years ago. The one thing I think people misjudged at the time is that Venter was never really after money; Celera was all about proving that he was smarter than everyone else. Which was probably true on a purely scientific level (although lazy; we could equally well claim that Celera was a waste of money because they didn't use third-generation sequencers), but didn't work out too well as a business plan.

There are at least a dozen other bits of half-truth and straight bullshit in the interview, but I need to sleep. Venter should stick to science and let someone else handle his P.R.

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3. Silas on July 29, 2010 10:41 PM writes...

Thanks very much for the link to that. I'm passing it around to like-minded friends; it's rather refreshing to see an uncompromising viewpoint honestly expressed.

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4. CurryWorks on July 29, 2010 11:32 PM writes...

Venter most likely does not like god because he is jealous that god beat him to creating life forms. If one goes for that in any case Venter does not like evolution for the same reason seeing that he tries to spend millions creating "synthetic life" with his e-mail encoded in his genome. Other than that nice guy as they are all nice guys

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5. student on July 30, 2010 12:15 AM writes...

Basically, I think he's right. Most scientists never give an opinion on anything, and only stick with the facts, because they're afraid of angering reviewers/colleagues who will impact their career, and it's refreshing to see someone give their honest opinion. Yeah, he comes off as arrogant, but doesn't he have a right to be with what he's accomplished?

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6. Andras Pellionisz on July 30, 2010 12:22 AM writes...

When the full human DNA showed up 20,000 genes as opposed to some expected 300,000 or more, there were some who actually learned something from it - and recognized that the fractal organization of DNA governs growth of fractal organelles, organs and organisms (FractoGene, Pellionisz, 2002). Today, consistently over 100,000 Google hits of "recursive genome function" with peaks of close to a million demonstrate that the message is sinking in for the second decade, that the fractal iterative recursion is the basis of genome regulation - and provides the clues for hereditary diseases caused by breakdown of genome regulation. Pellionisz_at_JunkDNA.com

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7. ALTheE on July 30, 2010 12:36 AM writes...

Craig is the kind of scientist people fear.

He's smart but has no morals and is a jerk.

It's not to hard to picture him working for Stalin.

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8. Andrew on July 30, 2010 2:41 AM writes...

@Nat(2)

For what it's worth, I never stopped thinking he was a self-aggrandizing jerk.

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9. RB Woodweird on July 30, 2010 6:41 AM writes...

ALTheE writes...

"Craig is the kind of scientist people fear.
He's smart but has no morals and is a jerk.
It's not to hard to picture him working for Stalin."

Yeah, you are all like 'oh, evil scientist' until that asteroid is headed for earth, then you come crawling back.

He may be a jerk, I don't know, but how do you know he has no morals? Because he doesn't believe in your Scripture?

It's not hard to picture you working for Stalin either, not with the NKVD van sitting outside your house keeping an eye on your family.

(Obligatory grad school joke:
Q: You find yourself in a room with Stalin, Hitler, and your PI. You have a gun with two bullets. What do you do?
A: Shoot your PI twice.)

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10. Anonymous on July 30, 2010 6:47 AM writes...

I'm a fan of a lot of Venter's work, but even I must admit that at times he seems like he's only an island fortress away from being a bond villain.

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11. bboooooya on July 30, 2010 7:19 AM writes...

"faith or science"

Really? I've never seen a discrete electron or neutron myself, but I believe that they exist.

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12. ogs on July 30, 2010 7:57 AM writes...

Faith and science ARE incompatible. In science, everything that you claim to know has to be based on solid physical evidence. If it doesn't, then you cannot claim that it is a fact, though it might be a hypothesis. Unfortunately, is not uncommon to see scientists clinging to hypotheses as if they were facts using a faith-like thinking mechanism. On the other hand the very foundation of religion is completely void of physical evidence. Religious people affirm that true believers have to live their religion 24/7. I agree 100%, and by the same token I think true scientists have to live their science 24/7.

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13. LNT on July 30, 2010 8:26 AM writes...

"SPIEGEL: Some scientist don't rule out a belief in God...."

Some? From the statistics I've seen and from my conversations with colleagues, I would peg it at around 50/50 amoung scientists.

The arrogance this man displays is just unbelievable. Who is he to tell scientists what they can or can't believe? There are PLENTY of us hard-core scientists that can rationalize how our faith can co-exist with modern science. Unfortunately, Venture just isn't quite smart enough to do the same....

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14. Wavefunction on July 30, 2010 8:30 AM writes...

I completely agree that Collins is now almost exclusively a government administrator. There may have been a time when he was doing some good science but that is long past. And even then, he was nowhere near as accomplished a scientist as Venter is.

I don't really care if Venter is a jerk (many brilliant scientists in history were). The man's revolutionizing science and that's what matters most right now. You may not always agree with him, but at least he is refreshingly candid.

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15. MIkeEast on July 30, 2010 8:32 AM writes...

@12. ogs

If that be the case, count me proudly as not-a-true scientist. I have no problem reconciling the two.

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16. Annette on July 30, 2010 8:34 AM writes...

I prefer scientists to stay out of my faith, just as I prefer theologians to stay out of my science. They are two different worlds.

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17. goldilocks on July 30, 2010 8:41 AM writes...

Off topic, but did you see this? Charles River is no longer buying WuXi... http://www.masshightech.com/stories/2010/07/26/daily54-Charles-River-pulls-plug-on-16B-buy-of-WuXi-PharmaTech.html

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18. Wavefunction on July 30, 2010 8:43 AM writes...

The question "Can science and faith be reconciled?" can be answered on two different levels. On one, practical level the answer is affirmative since many scientists in real life actually manage to reconcile the two in their minds. But in terms of methodology, no, the two cannot be reconciled since they differ radically in their methods and philosophy.

This may be one of those rare cases where two worldviews cannot be reconciled in principle but are routinely reconciled in practice!

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19. RickW on July 30, 2010 8:51 AM writes...

Collins cloned the human cystic fibrosis gene before the E. coli genome was sequenced. Not bad for an administrator.

People forget that Venter's shotgun sequencing approach basically failed for the human genome. They had to use the government's high resolution mapping data to finish the alignments.

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20. bad wolf on July 30, 2010 9:19 AM writes...

"Collins is just an administrator!" claims computer programmer turned businessman (turned self-proclaimed theological expert).

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21. DrJimbo on July 30, 2010 9:23 AM writes...

RickW's comment bears repeating.
This is one of the main things I recall from Sulston's book, he was amazed at the lack of acknowledgement of this from the private consortium. You'd think at this distance, Venter would be able to admit this, especially since he's moved on to other things, and with it being generally accepted that his invovlement did massively speed up the end of the genome project.
I've a lot of admiration for Venter but in this, it seems, he's a major ass.

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22. ronathan richardson on July 30, 2010 9:23 AM writes...

I guess i like Venter more after reading this interview than I did before. I mean most big-time scientists are such corny tools when they give interviews and speak in public--he gave real, true answers. However, he's an idiot on this synthetic cell work. Why he thinks that cells need to be synthetic to work is beyond me. He first has to figure out how everything in his basic organism works--this is the same work scientists have been doing on e. coli for ~75 years. And we're so very far from understanding how to build up a cell. He must know something that we don't.

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23. Anonymous on July 30, 2010 9:35 AM writes...

Venter spends the whole interview lamenting the lack of achievements as a result of the genome. Everyone else hyped it!! Then this passage:


SPIEGEL: The genome project has been called the Manhattan Project or Moon Landing of its era. It has also been said that knowledge of the genes will change the future of humanity and become a "main driver of the world economy."

Venter: Who said that? I didn't. That was the people at the consortium.

SPIEGEL: You're wrong. You made all those statements in an interview with DER SPIEGEL in 1998.


HAHAHAHAHAHAHAHAHA!!!!!!!!!!!!!!


SPIEGEL: You have complained about how naïve genome researchers were in the beginning. Will future generations eventually make fun of us in the same way for how naïve we still are today?

Venter: Only time will tell. Nevertheless, we now have what is going to be one of the most important tools for interpreting the human genome: the first synthetic cell. It will enable us to ask questions that would have been inaccessible before.


This makes sense. The key thing that we need to understand the genome is a microbe with synthetic DNA. Totally logical. What a brilliant guy.

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24. john on July 30, 2010 9:39 AM writes...

As an agnostic I ask, how much work has Mr. Venter done as a religious scholar. It's interesting how strongly we believe in our peer review system, basically saying you need to be an expert to understand and review our work as scientists. Yet many scientists feel they are expert enough in the area of religion to draw rock hard conclusions.

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25. Venter's cloaca on July 30, 2010 9:46 AM writes...

God? Ethics? Who needs 'em? After all, this is SCIENCE!

/sarc

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26. LeeH on July 30, 2010 9:49 AM writes...

Science is the belief that things are not black or white because of the evidence. And that belief is fluid.

Faith is the belief that things ARE black or white in spite of the evidence. And that belief is absolute.

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27. Annette on July 30, 2010 9:55 AM writes...

@LeeH--Interesting. I had no idea that I believed everything was black and white despite the evidence. Thanks for clearing that up for me.

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28. MTK on July 30, 2010 10:09 AM writes...

I was struck at the wording by the interviewer:

"Some scientists do not rule out a belief in God"

Heck, I'm essentially an atheist, but I don't rule it out entirely either. God, or at least type of god, could exist, IMO. Not in Venter's mind I guess.

Science and religion are the flip sides of the same coin. There's not as much difference as one might think. Both exist for one purpose: to explain the unexplainable. Each can be as dogmatic, adaptable, or absolute as their practitioners want.

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29. lynn on July 30, 2010 10:37 AM writes...

Not that it's a useful insight, but I was struck by how much Venter reminds me of Christopher Hitchens...both such secure atheists. I guess I like them for it.

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30. coprolite on July 30, 2010 11:27 AM writes...

Jean-Luc Picard: Q, what is going on?
Q: I told you. You're dead. This is the afterlife. And I'm God.
Jean-Luc Picard: [laughs scornfully] You are not God!
Q: Blasphemy! You're lucky I don't cast you out or smite you or something. The bottom line is, your life ended about five minutes ago, under the inept ministrations of Dr. Beverly Crusher.
Jean-Luc Picard: No... I am not dead. Because I refuse to believe that the afterlife is run by you. The universe is not so badly designed.

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31. g on July 30, 2010 12:30 PM writes...

Agreed with #30

Faith is a firm belief in something without compelling evidence. So from a scientist standpoint, things like God, heaven, hell, etc. haven't been proven or disproven. A cold-blooded scientist would have to be agnostic.
However, most warm-blooded scientists have opinions and gut-feelings, much like Venter wishes every scientist would have. A scientist having faith is doing what Venter wishes more scientists would do!

Since faith/God has neither been proven nor disproven, having a firm belief in the non-existence of faith/religion is as logically invalid as a firm belief in it. Therefore, Venter is a hypocrite and jackas*!

But he is a courageous, risk-taking scientist and we could use more like him.

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32. LNT on July 30, 2010 12:31 PM writes...

I wonder if Venture has ever taken the time to read Francis Collin's book "The Language of God". It's a fascinating read -- Collins does an excelent job of explaining how his belief in God and Darwinian evolution can (and must) co-exist.

IMO, one of the most profound arguements he makes is that our Darwinian origins do nothing to explain our sense of beauty and altruism.

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33. Anonymous on July 30, 2010 12:36 PM writes...

LNT, "The Language of God" is one of my favorite books.

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34. retread on July 30, 2010 12:52 PM writes...

Well, to accept that the complexity of cellular biochemistry arose by chance, just from purely random exploration of protein space, requires a faith that trumps anything in Genesis. For details see http://luysii.wordpress.com/2009/12/20/how-many-proteins-can-be-made-using-the-entire-earth-mass-to-do-so/. If you find anything wrong with the purely combinatorial arguments given there, please post a comment there.

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35. student on July 30, 2010 12:56 PM writes...

Forget the language of god...it's just a rehash of mere christianity by Cs lewis. Then he writes that he went on a walk and saw a frozen waterfall that looked like three ropes coiled into one and he decided that meant that the trinity must be true.

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36. victorypilsner on July 30, 2010 1:11 PM writes...

A dumb scientist with a bit more nuanced view

"What separates me from most so-called atheists is a feeling of utter humility toward the unattainable secrets of the harmony of the cosmos."

"In the view of such harmony in the cosmos which I, with my limited human mind, am able to recognise, there are yet people who say there is no God."

"Then there are the fanatical atheists whose intolerance is the same as that of the religious fanatics, and it springs from the same source . . . They are creatures who can't hear the music of the spheres. (The Expanded Quotable Einstein, Princeton University Press, 2000 p. 214)"

see http://www.spaceandmotion.com/albert-einstein-god-religion-theology.htm

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37. MarkySparky on July 30, 2010 1:32 PM writes...

This happens every time a high-profile scientist expresses strong negative feelings about religion. People come out of the woodwork to slander them, wailing about "non-overlapping magesteria" or some other nonsense. Who cares? This interview barely covered religion, other than to remind readers that Venter thinks Collins is a tool (I happen to agree). Venter's views on genomics as a medical tool are spot-on, despite his abrasive personality.

I think it is quite remarkable that somebody with so much invested (literally) in gene sequencing can dismiss it as a small/incomplete step. This is the guy who has "discovered" 90%+ of the known gene sequences (in a private project) and created the first synthetic genome. If he were as terrible as some say, shouldn't he be basking in the limelight, rather than dragging a water bucket through the Mediterranean? Real innovation requires people like Venter to cut through BS, not smarmy bureaucrats like Collins that see God in their Cheerios and think its profound...

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38. Anonymous on July 30, 2010 1:55 PM writes...

"Can science and faith be reconciled?" One can replace the other - see "Climate Science".

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39. Hap on July 30, 2010 2:10 PM writes...

Venter is a good reminder why scientists tend to stay quiet - 1) agressive opinions aggressively expressed don't substitute for thoughts, and 2) if what you've done is so darn good, then why does it require you to toot your own horn so loudly about it, like a photon field therapy or natural gamma-interferon? Oh, when your opinions aren't within your scope of expertise, then saying them loudly just gives you the chance to embarrass yourself in front of lots of people. (As a side note, if people aren't crediting you sufficiently for your achievements because they don't like you and think you're abrasive and self-aggrandizing, how is pissing them off going to gain you appropriate credit and honor? Is that the "When you're outnumbered, attack" theory of rhetoric?)

I sort of thought faith what what you had without data. Climate science has lots, while the "skeptics" have...what, 900 weathermen can't be wrong? Yeah, I think you've got your terms confused.

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40. daen on July 30, 2010 4:16 PM writes...

@retread: Interesting how some people are so happy to trot out combinatorial complexity arguments to dismiss the possibility of proteins arising through evolution (especially naive, error-filled ones that ignore the fact that it is not random but directed, that many functional proteins consist of repeated sub-groups, that many proteins share functional domains, and so on, all assumptions which prune the combinatorial tree by dozens of orders of magnitude), and yet do not blink at invoking the existence of an omniscient, omnipotent being of infinitely greater complexity to create these complex proteins ...

Something about swallowing camels while straining at gnats springs to mind.

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41. Tam2000 on July 30, 2010 4:39 PM writes...

I agree 100% with Wavefunction @18 that science and faith cannot be reconciled. How can a faith- absolute delusional disorder- be reconciled with science - explanation with evidence. Scientists can not have faith. In science there is no room for faith, every thing has to be proven or explained in a way that it does not violate other known facts. Until then it is only an unproven theory. In faith every thing is contradictory to each other. The most fundamental belief that there is a creator originates from the imagination that everything has and needs an origin. But then it contradicts itself that the creator does not need an origin. So the delusional minds can reconcile themselves but not with science.

Also there is a 'belief' that if you are not a believer you are immoral and arrogant. What a delusion!!

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42. CurryWorks on July 30, 2010 5:43 PM writes...

So the guy gave non-classical solutions to typically posed problems. If that is a metric of honor than using this logic the person that yells the loudest and insults the greatest number of his peers is honest and a good example of not being a "tool".

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43. REtread on July 30, 2010 6:35 PM writes...

#42 Daen: I am far from happy to trot out combinatorial arguments to dismiss the possibility of the present degree of protein complexity and structure arising by chance. I find many of the uses religion has been and is being put to absolutely horrible. I do not like where my arguments seem to lead. They need to be refuted (but I don't see how).

You need far more than 'dozens of orders of magnitude' to trim down protein space so all aspects of it can be explored. The current champ is titin with 30,000 amino acids, 300 modules of three types (1) immunoglobulinlike, (2) type III fibronectin, and (3) unique PEVK insertions. Even linking them together in any particular order is one in 3^300 possibilities, a number larger than all the baryons in the universe.

Only 1.5% of the genome codes for amino acids, but nearly all of it is transcribed, so proteins are only a small part of the story. Molecular biologists are fixed on proteins (they know lots about them, and the technology to study them has been developing for decades). But there is far more to the story. For just how protein-centric molecular biologists are see the current post about Autism Spectrum Disorder.

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44. Sili on July 30, 2010 8:12 PM writes...

He's smart but has no morals and is a jerk.

It's not to hard to picture him working for Stalin.


Morals? Who cares. I haven't seen him be unethical. (Collins, on the other hand, uses his position as head of the NIH to push his books on theology.)
I've never seen a discrete electron or neutron myself, but I believe that they exist.
Science: UR DOIN IT RONG. Why do you 'believe' subatomic particles exist? Because it was told to you from on high? As for Stalin, I think you need to look up Trophim Lysenko.
The arrogance this man displays is just unbelievable. Who is he to tell scientists what they can or can't believe? There are PLENTY of us hard-core scientists that can rationalize how our faith can co-exist with modern science.
Rationalise would indeed seem to be the operative word. And I don't see Ventner telling anyone what they can and cannot believe. What does do, is rightly point out that if you wanna call yourself a scientist, you cannot invoke supernatural forces as explanations. Science is perforce natural.
I prefer scientists to stay out of my faith
Kindly tell that to Collins.
turned self-proclaimed theological expert
[Citation Needed] As the Biologos link demonstrates, Collins is the one trying to do theology (at least John Polkinghorne became a vicar before trying to pontificate - not that that makes him right).
As an agnostic I ask, how much work has Mr. Venter done as a religious scholar. It's interesting how strongly we believe in our peer review system, basically saying you need to be an expert to understand and review our work as scientists. Yet many scientists feel they are expert enough in the area of religion to draw rock hard conclusions.
We need peer review in genuine sciences. You're using the Courtier's Reply to atheism. That we cannot understand the faithful unless we study sophisticated theology. This completely ignores the fact that the majority of the faithful do not believe in the gods of the sophisticated theologians, and that the good bishop Spong for instance, would be run out of most Southern Babtist churches as nothing but a blaspheming atheist. Secondly, I do not need to take an advanced course in Elfinology to say that in the balance of the evidence it is highly unlikely that there are fairies at the bottom of the garden.
God? Ethics? Who needs 'em? After all, this is SCIENCE!
What does God have to do with ethics? "Happy shall he be, that takes and dashes your little ones against the stones."
Science and religion are the flip sides of the same coin. There's not as much difference as one might think. Both exist for one purpose: to explain the unexplainable. Each can be as dogmatic, adaptable, or absolute as their practitioners want.
Really? How does science deal with evidence? How does religion? Has science expanded our horizons and technology? Has religion? Has scientists put dissenters in housearrest? Has religion?
A cold-blooded scientist would have to be agnostic.
But at some point it becomes pointless to insist that one is agnostic. Dawkins conveniently uses a seven-point scale on which he, himself, is a six. An atheist does not claim that gods do not exist. We merely observe that none of the gods so far postulated have been shown to exist. Deism is still a valid philosophical stance, but it is unscientific in that its god is outside the universe and unobservable - much like String Theory. I think you'd be hard put to find and atheist who would does not have a set of observations that could make them believe in gods. Atheism is eminently falsifiable. Religions are either already falsified, or have retracted into positions that make them unfalsifiable, and thus unscientific.
Francis Collin's book "The Language of God"
Is that the one he recollects how a frozen waterfall convinced him of the existence of a Triune God? (I seem to recall that passage has him kneeling in dew-wet grass - I'm not sure how that fits with the frozen waterfall theme.) (Oh, I see student has already confirmed that this is indeed the regurgitated Lewis. Carry on.)
Well, to accept that the complexity of cellular biochemistry arose by chance, just from purely random exploration of protein space, requires a faith that trumps anything in Genesis.
For fuck's sake, how hard is it to understand the bit about selection?! Evolution by Natural Selection is not a random walk. Replicaters proliferate proportionally to their ability to do so: better replicators - more copies, and so on. NOT RANDOM!
A dumb scientist with a bit more nuanced view
"I believe in Spinoza's God who reveals himself in the orderly harmony of what exists, not in a God who concerns himself with fates and actions of human beings." Amusingly enough I took that quote from this page about why Einstein is wroooong. With the invocation of Spinoza (quite an interesting heretic, really), Einstein can at best be called a Deist. I think you'll find that most of us atheists are indeed awed by the beauty of 'Creation'. We just do not feel the need to cheapen it by trying to fit it into everyday boxes. How much greater is the creation when the creator is unskilled? Is not the greatest creation that which has no creator? And if we go back the Spinozan view of God as the sum of the laws of Nature, then I kindly ask you to show me someone to prays to the Law of Gravity.
I think it is quite remarkable that somebody with so much invested (literally) in gene sequencing can dismiss it as a small/incomplete step.
I think what he dismisses is the puffed up rhetoric about how the human genome would allow us to fix all illnesses within the decade. (And of course "language of God" that Collins got Clinton to put in his announcement - how's that for "non-overlapping magisteria"? Funny how that only goes one way.) The HGP has had a big impact on basic science, but the much touted practical applications are indeed nonexisting.
"Can science and faith be reconciled?" One can replace the other - see "Climate Science".
See Hap for details. Sticking your fingers in your ears and chanting "LALALALALLALALLAAAAA" does not constituted a sound argument.
Molecular biologists are fixed on proteins (they know lots about them, and the technology to study them has been developing for decades).
Are you seriously completely unaware of all the research into gene expression and silencing? We know there's more to it than proteins. Not everyone was surprised humans turned out have 'only' 20000 genes. (Collins may have been, though.) We know it's about how, when and to what degree those genes are turned on and off.
You need far more than 'dozens of orders of magnitude' to trim down protein space so all aspects of it can be explored.
I'm frankly not sure what you're trying to get at here, but it's complete irrelevant how many combinations it would take to make a modern protein from isolated amino acids. Noöne but creationists claim that modern proteins sprang into being fully formed. The whole friggin point of evolution by inheritance is that we can start from very simple replicators who in time can grow into awfully complicated interlinked systems. Secondly, while I'm no expert in abiogenesis, I seem to recall that most researchers say that some sort of RNA-dominated world of replicators preceded our current proteinbased life (as evidenced by the ribozyme for instance). But, again, noöne is saying that the very first replicator was RNA. There are some interesting hypotheses involving simple micelles of ambitheric molecules that might go through a growth-division cycle in the vicinity of deepsea vents. Permalink to Comment

45. andrew on July 30, 2010 8:40 PM writes...

@ RB Woodweird

Big shock a jerk is admired by other jerks who like to lie and twist the truth.

ps your joke is unoriginal crap.

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46. Anonymous on July 30, 2010 8:51 PM writes...

really insightful.

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47. Anonymous on July 30, 2010 8:52 PM writes...

really insightful.
Thanks a lot.

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48. Wavefunction on July 30, 2010 9:27 PM writes...

Daen is right. I thought we had already made headway into addressing the combinatorial arguments against protein structure and function. Once we accept the co-operative nature of self-assembly, things begin to look much more reasonable. Even a computer program like Rosetta (which is considered state-of-the-art as far as predicting protein folding is concerned) can pare down the vast space of possible protein folding intermediates to a manageable few by using well-established motifs from known protein structures. If this can be done in a few hours by a computer program for a decent-sized protein, I don't see why it would require an act of faith to believe that nature could implement such a strategy over billions of years.

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49. retread on July 30, 2010 10:04 PM writes...

#47 Wavefunction: Of course Rosetta can do this. It starts with proteins which already are known to fold into one shape, to find the how another protein (which is known to have one shape) folds into it. Rosetta is basically starting with the answers in hand, and a question which is known to have an answer.

I've got to get some stuff I posted on the Skeptical Chymist back when I was writing for them up on my site for you folks to chew on, but I'm going to be visiting family until the middle of next week. In the meantime have a look at http://luysii.wordpress.com/2009/11/29/time-for-the-glass-eye-test-to-be-inserted-into-casp/.

If mutation is truly random (and it seems to be) I don't see how nature has the time, space or mass to "do it".

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50. fred on July 30, 2010 10:32 PM writes...

I am FAR more offended by politicians who talk about their "Christian faith" than thinking people who espouse their lack thereof. We're living in a country where some school boards have tried to toss out Darwin and women have to put up with all kinds of paternalistic nonsense from legislatures who feel they oughta have more control over a woman's body than she.

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51. Streuth! on July 31, 2010 5:05 AM writes...

Science IS a religion!

Not just jealous but young and insecure.

And one that still wonders whether it is going to survive...


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52. daen on July 31, 2010 5:09 AM writes...

@retread: You're missing the elephant in the room, which is so often overlooked by those who invoke a purely combinatorial approach to questions of how functional biological systems arise. The elephant is that all proteins do something useful, which is non-random. A naive combinatorial approach based on pure random chance does not take into account the equally sound physical principles of natural selection, which is anything but random. An organism alive today exists in a state of extreme adaptation, from its gross morphology down to its molecular biology. Working backwards, at every step of the way, its ancestors survived. Mutations conferring an adaptive survival advantage upon those ancestors can be traced backward, generation by generation. Other mutations, which may have been deleterious or which did not confer sufficient advantage, have been lost. Surely you know this; it is at the heart of the modern evolutionary synthesis. So to invoke a pure random chance argument and express surprise at the vast numbers it throws up is incongruous and, worse, plain wrong. Your argument is utterly specious.

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53. CELLBIO on July 31, 2010 5:04 PM writes...

Sili,

Thank you thank you thank you. I didn't have the energy to respond and appreciate your effort.

For those that persist in 'believing', try the His noodly goodness, the Flying Spaghetti Monster. the logic is impeccable for those with faith.

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54. andrew on July 31, 2010 6:21 PM writes...

"Morals? Who cares. I haven't seen him be unethical. (Collins, on the other hand, uses his position as head of the NIH to push his books on theology.)"

It seems you care about morals but only when you think people you disagree with aren't in agreement with them.

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55. Joseph Hertzlinger on August 1, 2010 1:37 AM writes...

Reply to # 12:

Faith and science ARE incompatible. In science, everything that you claim to know has to be based on solid physical evidence.

Speaking as a mathematician...

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56. LeeH on August 1, 2010 10:48 AM writes...

@retread: For a simple concrete example of how good solutions to problems that are seemingly infinite can be generated "randomly" simply Google genetic algorithm solutions to the travelling salesman problem.

Briefly, if a salesman has to travel between multiple cities and you want to know the best (i.e. shortest) way to do it, once you consider a rather trivial number of cities you are considering, if done exhaustively, more possible paths than there are atoms in the universe. Yet, using "random" selective methods (such as GAs) you can have Excel generate good solutions in a matter of minutes.

Perhaps this implies that God is somehow, in a divine, intelligent way, extending his mighty hand into Microsoft's product. A more likely explanation is that invoking combinatoric arguments, without truly understanding combinatorics, is not the way to refute the conclusions of thousands of man-years of consistent evidence.

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57. DV Henkel-Wallace on August 1, 2010 11:08 AM writes...

Can we stop with the "read the genome" meme already. We can finally transcribe it, which is a key step in learning to _read_ it, but only one step. Venter even admits this, but clearly says we don't understand the "semantics" yet.

Sorry, this is just a pet peeve, but I think the use of "read" misleads a lot of nonscientists.

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58. Anonymous on August 1, 2010 4:29 PM writes...

Hey, give Ventner a break. He's a top notch scientist. He changed the landscape. However, the landscape ain't stationary. Case is point, who would have thought that "french fries" could cause cancer???? Remember, the acrylamide stuff in 2002-2003, Interesting. Below the radar but no one ever realized it. My point is that there are so many "un known's" out there. Perhaps if you happen to swallow some mouth wash after downing a coffee then your risk of cancer could increase. Remember, what we don't understand is primarily what we dont know!!

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59. Anonymous on August 1, 2010 6:54 PM writes...

Ahem! Fellow scientists:
Lets get on with *living* in the real, *material* world, and invent some new blockbuster drugs and maybe *win back* the Nobel Prize for Chemistry!

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60. RB Woodweird on August 1, 2010 9:26 PM writes...

andrew writes...
@ RB Woodweird

"Big shock a jerk is admired by other jerks who like to lie and twist the truth.

ps your joke is unoriginal crap."

Dearest Andy,

Lying? Twisting the truth? We like to call that "submitting our results to a reputable journal".

And that was no joke. It actually happened.

swak

RB Woodweird

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61. bad wolf on August 1, 2010 10:01 PM writes...

Must we have the same retarded discussion whenever someone mentions their faith or lack thereof? Apparently so. Must we credit scientists with insight into areas they have no expertise? Apparently so. Must we slap ourselves on the back for our amazing insights into the human condition?

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62. Morten G on August 2, 2010 1:09 AM writes...

Assuming the existence of God (for the monotheistic - gods for the polytheistic), what is the argument for praying to/ worshipping God? That you have faith that it is the right thing to do? Or that it says to in the Bible? Because as scientists we must all be able to agree that the bible can't be interpreted literally.

Oh and Sili +1

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63. Sili on August 2, 2010 4:04 AM writes...

It seems you care about morals but only when you think people you disagree with aren't in agreement with them.
Pardon? Permalink to Comment

64. sgcox on August 2, 2010 7:38 AM writes...

Sili: it means he likes what you say (I think)

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65. Bzh on August 2, 2010 1:43 PM writes...

If you want to read more about Venter, Collins, Watson and a few others, I would strongly recommend reading the following book: "Masterminds: Genius, DNA, and the Quest to Rewrite Life". Each of them talk about their work, their convictions and the future. It is provocative, entertaining but also really fascinating as you get to discover the personalities of these scientists. Here is the link on amazon if you are interested: http://www.amazon.com/gp/product/product-description/0060537396/ref=dp_proddesc_0?ie=UTF8&n=283155&s=books

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66. Aspirin on August 2, 2010 2:11 PM writes...

-Must we credit scientists with insight into areas they have no expertise?

No, but there's also no need to credit theologians or religious people with such kind of expertise. Why exactly is a religious person or theologian more 'qualified' to talk about morality than a scientist for instance? Just because science does not have the answer to certain questions (yet) does not mean someone else has them.

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67. geezer on August 2, 2010 2:11 PM writes...

It's clear from the interview that Venter is an uber nob (being caught in the quote gaff was fantastic) but he's a very good scientist and businessman. Hey, if my job had me sailing around the Med and sequencing whatever crap ended up in my net, I'd have thought I died and gone to....ehhh let's leave that alone..

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68. Wavefunction on August 2, 2010 2:15 PM writes...

@Retread: The point was that Rosetta uses a mix-and-match strategy which makes the conformational space required to be searched much smaller than what would result from random search alone. Nature proceeds in a similar way, non-randomly accumulating pre-existing fragments from known protein structures. It would indeed be miraculous if it were purely random. But it's really not, and this argument is quite well-trodden.

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69. idiotraptor on August 2, 2010 6:55 PM writes...

The God vs. Science response string is thoughtful as well as, entertaining. I'll refrain from jumping into the fray here since the matter has been discoursed upon ad infinitum since the Enlightenment. Rather, I have comments Venter's tone. He is dismissive and belittling of Sulston and Collins, respectively. Yes, Venter is an accomplished scientist and emtrepreneur. However, my perception from reading the Speigel interview (and previously published comments by him) is that he is insufferably arrogant and devoid of any humility. I suspect he extolls intellectual acheivement as the principal measure of personal worthiness and that he has no respect for anything beyond his own views.

His scientific and entrepreneurial successes will be cited for a long time, but he's a boorish asshole. The guy probably has no genuine friends.


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70. srp on August 2, 2010 8:36 PM writes...

I'd like to step away from all the theology fur fights and ask some basic science questions.

1) You can't predict Venter's eye color from his genome? So everything they teach in high school genetics is BS?

2) If human diversity has a genetic component--i.e., two genetically different embryos subjected to the exact same environment would differ in phenotype--then how can we reconcile continuous distributions of phenotype traits with a small number of genes? Even if they regulate each other in complex ways, in the end some exogenous variation must lie at the head of the causal chain, and if that variation can only take on discrete values then the output ought to have discrete values.

3) An exception to the argument above is some sort of symmetry breaking in the regulatory loops of genes. If the system is only unstable, like an ice cream cone balanced on its point, then any random jiggle would cause a given organism to "tip" into a particular configuration. This explanation would allow for a continuous trait distribution.

4) Is there anything besides symmetry breaking that could explain continuous phenotypic variation from a small number of discrete genes?

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71. Toluene on August 2, 2010 10:29 PM writes...

Reply to #70

Epigenetics can explain many of the points in your question where identical genotypes can give rise to different phenotypes. We are just starting to understand how modifications of the histone code affects gene expression. For a great website for epigenetics see http://learn.genetics.utah.edu/content/epigenetics/inheritance/

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72. Cellbio on August 2, 2010 11:23 PM writes...

srp,

First, think not only, or maybe not even with first priority about 'loops of genes' but rather about proteins interacting with the environment, and transmitting signals inside the cell. Then invoke regulatory networks and cell-interaction and the complexity is great.

Then, you must invoke, in the non-model system that is the real world, an interaction with the environment which varies in degree (concentration, time) and complexity (covariables that influence the phenotype) and not well represented by thinking in terms of discrete values.

For example, imagine two patients with different genetics, or alternatively identical twins, encountering loss of tolerance and developing autoantibodies. The process that culminates in antibody titers may involve exposure to a pathogen, virus or bacteria, that blocks regulatory cell function, creating an opportunity for self reactive immune cells to proliferate. Length of pathogen exposure, nature of agent, innate immune system function may all vary, by genetics, or even amount of stress or by lack of sleep within identical twins, not too even mention selective allele silencing. The immune cell activation events require presentation of self antigen, which requires proteolytic processing and costimulation with signal strength a key variable. More room for non-discrete outcomes. And we haven't even factor in physical barrier function, diet & sun exposure (vitamin D status) and random variation in intermolecular interactions in complex systems. So even if the same amount virus entered, was there also a dendritic cell nearby? If the DC produced cytokines, were the effector cells in range at that time? There is no reason these would be the same in the same individual at different times.

So, my perspective, as a biologist, is that discrete outcomes like seropositive status, serves us well from a clinical diagnostic standpoint with highly sensitive assays for infectious agents, but is generally very poor for interpretation of most biology. My experience with clinical trials, as others will also attest, bears out this tough point: humans vary more in biological response than is useful for pharmaceutical development. Yes/no outcomes would be a dream, but unfortunately they are far from reality.

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73. mad on August 3, 2010 11:11 AM writes...

What Derek extracted is in the interview but its really just spice to catch people’s attention.

The true message from Venter is that many scientists are wasting time and money with inefficient work particularly those on the government payroll.

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74. srp on August 4, 2010 5:37 AM writes...

Cellbio:

Thank you very much for your response. I get the general drift of it.

Most of your suggestions start with environmental exposures of different sorts, and I get that. I was asking about different genomes in identical environments, the opposite of the identical-twin setups, but your point that environmental influence really isn't uniform in any real situation is well-taken.

You also mentioned "random variation in intermolecular interactions in complex systems," which is kind of what I meant about symmetry breaking. And then there is your fascinating point about which cells happen to be in range of a particular virus when it enters the body, which never would have occurred to me.

So is it really true that you can't read off the genome to predict eye color? And if so, should we stop providing oversimplified explanations to biology students?

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75. coprolite on August 4, 2010 9:57 AM writes...

if I might interject my thoughts, as a biologist turned resentful chemist, I think that everything in bio 101 is oversimplified, those courses tend to cover a wide range of topics and only gently brush the surface of each. I think this is necessary, because if one advances the ideas too quickly you'll lose everyone along the way. the eye color analogy is necessary because it makes the concept tangible, the caveat I think is to realize that it was bio 101, not the research of a functional laboratory.

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76. Cellbio on August 4, 2010 8:24 PM writes...

I am not sure what stories are offered about predicting eye color from sequence data but do recall that the genetics, in the classical sense, of eye color was a staple of the 101 type classes. I remember the lesson being illustrative of recessive alleles carried by each parent could produce blue eyed kids from brown eyed parents. I kind of liked it because I could refute my older brothers story of my adoption.

Coprolite dropped a solid rationale for starting simple and adding layers of complexity. I like this model of scientific education.

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77. retread on August 10, 2010 9:37 AM writes...

If you thought comments 34, 40, 43, 48, 49, 52, 56 and 68 were interesting, follow the #34 link, and continue the discussion. I apologize for nearly hijacking the discussion here.

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78. seance photo on June 19, 2013 11:32 AM writes...

Only wanna input that you have a very nice internet site , I like the pattern it really stands out.

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